Amongst some atheists there is a very vocal and often aggressive anti-religious stance. In particular when G.W. Foote created The Freethinker journal he did it with the "chiefly aggressive" purpose to "wage relentless war against superstition in general, and against Christian superstition in particular.". These are pretty strong words and some critics (mostly religious though some atheist and agnostics as well) attack known anti's, such as Richard Dawkins and Christopher Hitchens, as being intolerant to an extent that is zealous.
The above atheists are very clear in their personal view that the world is a better place without supernatural and organised religion (note this is normally aimed at the Abrahamic religions) and that these religions are a large cause of many of societies issues. The problem, especially for Christians, is that they don't have a very good track history to refute this claim with some of the most awful atrocities over the last 2000 years attributed to a Christian belief - including, of course, the Spanish Inquisition, Witch Hunts and Nazism - "The work that Christ started but could not finish, I--Adolf Hitler--will conclude" to name but a few.
Even dismissing historic events atheists often take issue with the Bible's teachings itself; to start the Bible records God's death count of over two and a half million and credits Yahweh for some extremely awful moral atrocities including (but not limited to): God's instruction that natural disasters are his wrath, genocide and ethnic cleansing, human sacrifice, condonance of slavery, the general treatment of women, claims that God himself is evil, the strange demands to eat feces and overall having more passages to do with killing than love.
Furthermore the Bible doesn't seem to display much tolerance to those who do not believe in God or Christ repeatedly calling for, and carrying out, their death; Jesus himself calls for all non-believers to be slain before him and curses those who disbelieve his miracles to hell. The old testament is equally harsh calling for non-believers to be hounded out and stoned to death, including family members and even whole towns (including livestock) if non-believers are discovered amongst them. Note that these passages are not limited to the Old Testament as some Christians have argued and even if they were that does not necessarily exempt them and some willingly follow their example.
Some would argue that this is all in the past and modern religion in a great framework for promoting strong morals yet many theists are way out of step with current moral values and religion is often used as a means to prevent progress on ethics. Today, in the developed world, religion is used to justify strong prejudices on sexuality, and gender to the extent that in most secular countries organised religions are often except from discrimination laws (note the wording as "circumstances where an employer may discriminate"). There are also still a significant number of Christians who subscribe to the Biblical view points.
Does the fact that religion gives justification to moral stances which would be ironically viewed as reprobate by your average atheist justify atheists apparent intolerance? After all many religious leaders spread the message of love and peace. One of the common arguments is that the moderate religious leaders actively condone these prejudices, despite the Church of England's 'progressive' attitudes on ordinating women many organised religions still do not allow it and still officially site homosexuality as a sin and even under circumstances where the position on sexuality and gender is soften it is still very weak compared to modern values and even the so called progressive such as the CofE are still found guilty in a court of law of prejudice. It is argued that this attitude from the leading groups give acquiescence to the more extremest views: after-all the Church does not outright condem these prejudices, instead it sights itself as exempt from them so therefore anyone who is a follower of that religion is also exempt from that prejudice. The argument is that because the CofE and the Roman Catholic church etc. do not step up to the pulpit to condemn such views then the more extreme element can get away with sites like these: GodHatesFags.com, GodHatesAmerica.com, GodHatesCanada.com and GodHatesSweden.com, the same charge is continuously labelled against Muslims by our politicions.
The danger is that if atheists pursue a strong non-religious agenda do we not end up with even more atrocities such as those committed in the name of communism? Amongst intelligent people there is no danger here as the vast majority of atheists do not promote violent eradication of religion or immorality (in fact I know of none that do) but instead believe in education and in particular the promotion of true secularisation which promotes the freedom of religion but instists on its seperation from state (removal of religious schools, religious laws etc.). Even the most outspoken atheists such as Dawkins would never condone prejudice against peoples personal beliefs but believe that religion should not be given any special status in secular society, especially in law, and especially in terms of argument. It is this strong view, especially with books such as the God Delusion, that religion should not be protected from ridicule and criticism which seems to upset a lot of theists who promote the intolerance claim. Atheists argue they are attacking an idea, like Communism or Conservatism or Capitalism but many theists believe that to attack their beliefs is far worse than attacking an idea (and in fact classing their belief as merely an idea is an attack in itself). The problem lies in the concept of blasphemy which - though mostly focused in the media on Islam is no less viewed by Christians - as the Bible clearly states is a sin punishable by death. The basic problem lies in the example that where a humanist vegetarian is 'merely' offended by the eating of meat on personal ethical grounds to a Jew or a Muslim the eating of pork is the breaking of their religious law and therefore the word of God. To criticize the vegetarian (even if they are the anti-christ) is acceptable but to criticize someones religion, though not entirely blasphemous, is still to attack the word of God, therefore the religious doctrine stands above the personal ethical desicion. This of course becomes ridiculous as the follower of one religion believes itself correct over all others yet by definition of the fact that their beliefs differ are in open criticism of each other, so a Christian has no issue in blaspheming Mohammad - and in fact almost actively has to in order to deny him - just as a Jew does Christ. The fact that blasphemy laws still exist in many countries including the UK does not help this issue.
"Tolerance is only another name for indifference" - Somerset Maugham. Everyone has the right to believe what they want, on that nearly all atheists agree (even if the Roman Catholic Church doesn't) and, unlike some of the religious, atheists do not see those people with religion as inferior citizens, human beings, or inferior intellectually or suggest they have less rights (including their rights to believe) or less/more capacity for love or that they should be imprisoned for their beliefs (or sexual preferences). Atheists respect (and instist) your right to believe they just may not respect what you believe, in a twist on Voltaire "I may not agree with what you believe, but I will defend with my life your right to believe it." but like free speech the atheist also reserves the right to criticize and disagree. The definition of intolerant is as such:
a) Unwilling to tolerate differences in opinions, practices, or beliefs, especially religious beliefs.
b) Opposed to the inclusion or participation of those different from oneself, especially those of a different racial, ethnic, or social background.
By this definition atheists are not intolerant as they are neither unwilling nor opposed to those concepts, even the FreeThinkers strong words do not call for the eradication or forceful prevention of religious thought but instead:
"It will do its best to employ the resources of Science, Scholarship, Philosophy and Ethics against the claims of the Bible as a Divine Revelation; and it will not scruple to employ for the same purpose any weapons of ridicule or sarcasm that may be borrowed from the armoury of Common Sense."
The language is colourful - deliberately biblical - but the 'war' is only in terms of intellectual argument and nothing else and although it is offensive (I myself often feel the FreeThinker goes too far) it is debatable if it crosses the line to intolerance.
To conclude atheists are not intolerant to religion; atheists disbelieve, criticize and disagree with religion, atheists may class religion as silly, irrational, delusional or even dangerous, some atheists believe that religion should have no special rights, privilages or exemptions (including religious dress in schools) but they do not seek to change, silence or suppress people with religious views.
The opinions on the linked websites and are including as evidence to the arguments I have presented and are not necessarily my own and should not be used as indication of my opinion or the opinion of any other group, religious or otherwise.
I would also like to say that although many of the arguments I have put forward place religion (especially Christianity) in a negative light this is not a reflection of any individuals interpretation of the religion and many Christians would feel as equally upset by these sites as any non-believer would and may also feel misrepresented by the authors of those sites.