I don't think that anyone doesn't think we are free to believe what we want.
We are also free to believe what another believes is offensive, or nonsense.
I would first differentiate between Christians. I think there is an important distinction between what I would call literal fundamentalists; those who take the Bible literally and have very 'traditional' interpretations of what the Bible means and what god is, and more liberal Christian thinkers.
That later group and the athiestic lobby rarely argue in the way the first group and athiests argue. A liberal christian and an atheist can agree on many things - apart on the existence of god, which they'd probably agree is undeterminable (although both would still feel their opinion on the existence of god was more valid than the other's).
I suggest that the difference in paradigms between atheists and literal fundamentalists is the main cause for conflict.
Literal fundamentalists to an atheist believe in utter nonsense; to literal fundamentalists atheists are the enemy and have been decieved, probably due to their own wanton desires.
A second reason is the (and I stress this is opinion) misconception some people have; this is not a soap box, for all that some use it as one. Some people object to the very fact others disagree with them in a forum for discussion.
People can disagree with me about evolution until the cows come home; I am not insulted or bothered by it, in fact I enjoy the debate. The criticism that certain literal fundamentalists might pour on those beliefs means nothing. If someone has a belief in ghosts and someone criticises those beliefs, then they seem far more likely to be offended. This is in part due to the fact that the paradigm they use is one relying on personal experience rather than one more relaint upon evidence, and as such doubters doubt THEM. If an atheist is doubted it is the facts of their argument that are doubted; it's less personal.
As such I believe that a certain amount of oppostional discourse between the above two paradigms or lobbies is inevitable as it is implicit in the characteristics of those paradigm.