You know, we're almost getting into "no true Scotsman" here. There are atheists who want religion to die out by persecution (the "make them second class citizens" ideas seem to be very popular here on Slashdot), and there are atheists who are like you are describing, who only want to persuade people. I have no idea what the relative proportions are between the two groups.
By the same token, there are Christians who want to infringe the liberty of atheists, and there are Christians who find that completely abhorrent.
To complicate the issue further there are all kinds of disagreements about what actually constitutes persecution and aggression. The issue of educating children is a prime example - some people feel that that responsibility lies primarily with the parents, and some feel the children are more the property of the state/society. This is on both sides of the argument - many want to use the schools to promote religion, and many want to use the schools to demote religion and counteract religious instruction from the parents.
There are lots of other examples, too. Many Christians are utterly totally blind to the fact that laws against consensual sexual behavior or against alcohol are a complete violation of liberty. I could go on and on.
I wish we'd all agree on the leave each other alone / everyone change their minds by respectful voluntary persuasion position. But that's probably a pipe dream.