Generally, I realize it is bad form to call someone stupid when they make a bad decision based on erroneous information, or my favorite, saying something without due thought. After all this person may have an IQ like Einstein or be walking around with 6 PhD's. Although, I will be the first to admit that IQ is not a true test of what people call smart. However, everyone makes mistakes and when we do we should be able to call that person stupid. I even call myself stupid when I make a mistake.
So let me ask again. Why can't we call theist's stupid? If this person has never been confronted with any evidence whatsoever for the lies, paradoxes, irrational thought, inaccurate history that religions portray, then I agree calling them stupid is not the best idea. But lets be frank, those are not the people atheists are calling stupid. We are calling the people stupid who cling to their beliefs after more explanations than a child requires to learn how to use the toilet properly.
So in conclusion, just as we call some people crazy for believing in UFOs we should be able to call some people stupid for their belief in a god.
Here is an interesting documentary on the word stupid and its implications. It's very long, so all you need to know is that the first step to recovery like with most things is admitting you are wrong and accepting you acted stupidly.