annoying reason #1:
"That is stupid."first, let's get the terms right... stupid means to lack ordinary keenness of mind... it comes from the Latin, stupere; to be numb or stunned... it is a pejorative, implying that the person lacks the capacity to reason at a level of the ordinary individual... this kind of argument is used to belittle the target, usually in an effort to raise the attacker's sense of self worth.
often, what the atheist is attempting to say is, "You are incorrect due to your ignorance of other information which contradicts your viewpoint"... but they don't say this... because it can be easily turned on the attacker in the form of, "Present this information for consideration and debate"... this often ends with showing the atheist as being ignorant of their own facts, and woefully ignorant of the defense's facts.
the ideas which the atheist defines as "stupid" are concepts which require deeper understanding than most people, atheist and religious alike, are willing to achieve... for example, people often think it is stupid to believe in something which cannot be observed... yet they readily accept much of science, even though much of it cannot be observed... we cannot see quantum particles, yet through their effects we believe they exist... by scientific method we determine that these particles have certain properties... so, using indirect evidence, we believe in electrons and leptons and quarks... we construct our beliefs around them, even though we cannot see them.
the only thing more stupid would be to dismiss something on the basis that you cannot discern it... while you'll often get the Flying Spaghetti Monster response, you should (gently) remind people that almost all of science depends on an open mind... bacteria, atomic energy, and most of modern science had to pass through respected scientists who sternly said it couldn't be seen and therefore did not exist.
dismissing other viewpoints, including the theistic, is a sure sign of stupidity.