I feel the OP is, quite honestly, relatable to a lot of what many people have witnessed and discuss comes from the ranks of Christianity - maybe not all denominations/sects - but enough of them. Especially taking into account history. How long was it before many facts were incorporated into the base of accepted knowledge, and what ended up being the biggest opponent to such incorporation much of the time? How about all that music people were encouraged not to listen to? Don't play Dungeons and Dragons, right? Also gotta make sure you're wearing the right clothes! "Stay away from even the appearance of evil."
Sure... there is anecdotal evidence to the contrary, obviously. We all know "not everyone is the same", etc. And seriously... is it of absolutely no use to talk about something in general terms when it is something seen a relatively high proportion of the time? Not all dogs attack people viciously, but we still tell our children to "be careful" around them, don't we? Everyone is always on everyone else's case, but generalization has its purposes. It only "sounds good" when you decry it as an offense because it's an easy target... because "we're all special."
Personally, I honestly like to hear what people think of "all atheists." The things they complain about. Then I can either refute if I think it's baseless, or accept it if it's not and vow to make sure I, personally, don't make the same trespasses. Or accept it and simply decide not to care that other people are bothered by the behavior, etc. At least I am informed. I'd always rather that than the alternative.