Usually, it is not going to be productive to simply call someone "stupid".
I think you are grouping too many things together, or you are not writing with adequate precision. It is not stupid to think that there might be aliens somewhere in the universe (as it may have similar causes to life here), but it is an entirely different thing to suppose that every unidentified thing that flies is an alien, which would be stupid, as there is no reason to believe that. (If I am wrong about that last point, naturally, someone may point it out if they wish, by providing the evidence for the claim.)
Who are the "we" you are referring to? I am quite willing to say, of anyone who believes things without evidence or contrary to the evidence that they have, that person is being stupid with regard to that thing.
I find it funny that my attitude on this point is associated with atheism, as that suggests that theists have no good reason for their beliefs at all, and that everyone knows this. No theists should be afraid of looking at evidence fairly and objectively, unless they really believe that they are believing a lie and want to believe a lie, which is a very peculiar thing, as it suggests that deep down somewhere they are really atheists themselves.
A.J. Burger makes an interesting point that relates to this:
burger-book
What is particularly odd about this is the fact that many people say that these matters are the most important things in the world, and yet they generally are so careless about them. Many people are not very consistent about these things at all, and consequently they are necessarily wrong, no matter what the truth might be. It is a curious thing, when one purports to want to find great truths, to choose a course of action such that one guarantees failure no matter what the truth might be. It is odd that so many people, who are smart enough to look both ways before crossing the street, are so careless about what they claim is infinitely more important, the fate of their immortal souls. I would say that that shows great stupidity.
Who said that they should be treated differently? Of course, it is a different subject, and so there will be some differences that will result from that, but otherwise, I see no reason to regard the one as different from the other. In both cases, it is all a question of evidence and reasoning, whether the person is being stupid about the matter or not.
It is unlikely to be useful to simply call people "stupid" without any kind of argument given. In most cases, it is best to simply comment on the arguments and not comment on the stupidity of the arguer, even though believing based upon fallacious reasoning is stupid, as far as that point goes.
I suppose I may as well add, that pretty much everyone does or believes something stupid occasionally, but to do so habitually is what causes one to truly deserve being called a stupid person. Perhaps that is a source of some issue you have with what I have been saying, though I tried to head that off with my previous comment about a person being stupid about one thing does not necessarily mean that that person is stupid about everything else.
