I've wondered that myself, particularly in regards to the recent evolution vs. "intelligent design" debates in school as of late. I'd be interested to here what other HN readers think.
This is the most dramatic instance I experienced, but in Honors English we spent at least a week on the Bible, but never any other religious texts. Conveniently, at the same time I had read some vampire fiction by Anne Rice and concluded that it's possible that Satan is actually the hero of the Adam & Eve story. It turns out, however, that this is not a good opinion to express when trying to do well in English in a conservative public state school.
As to Earth Science, I was not penalized for my response; had it been, this would have been clearly objectionable. On the other hand, at the time I did feel that it was unfair in that one could give what I considered a cop-out answer for full credit. It may be a theologically true response, but it does not give us any scientific insight and understanding into our Universe.
Given the two examples above, I'm not really sure. It can certainly be uncomfortable for someone who is brought up as an atheist, but I'm not sure it's outright illegal. And this is where the avenue for standardized testing comes in -- it's not necessarily to demonstrate student learning but perhaps rather to better identify egregious issues in school districts.