Oddly enough, a lot of people equate the idea of something being secular as being the same as it being atheist. I've heard of people complaining that by removing compulsory school prayer, that you're making atheism a state religion.

But they're not nearly the same thing. Being silent when it comes to religious matters doesn't imply agreement with atheism, nor does it imply agreement with theism (or polytheism, for that matter). And by saying something, such as a football game, or graduation, is not a proper place for religious speech doesn't mean they're degrading that speech - after all, one would assume they'd be consistent and keep anti-religious speech out of that venue also.

The easiest way to treat something as volatile as religion fairly is to not treat it at all. Just because the government is not supporting or showing preference for your religion doesn't mean they're trying to discourage it. This isn't a case of "if you're not for it, you're against it."