If Atheists were seeking to abolish religion directly, say by burning churches or murdering clergy, then yes, that would be a violation. Saying that religion is irrational is no more a violation of the freedom of religion than saying that 2+2=4 is a violation of your right to free speech if you say that 2+2=5. As Spider has pointed out, it's a matter of rationality.
There is a great difference between violating a person's right and choosing to point out falsities in their thinking. Certainly you have a right to believe whatever you want. That is an unalienable right that all humans possess. Every single person, however, also has an unalienable right to search for logic, rationality, and truth. It is only natural to discuss these things in a debate format and to attempt to persuade others to your side of belief.