Because if they had no helmets that would've been stupid, and that is obviously something the average movie-goer would criticize.

So your argument is "the average movie goer is too stupid to notice"? I already said that.

But why set the bar so fucking low? It would cost the movie nothing to have them either keep their helmets on, or hang a lampshade on the fact that taking their helmets off could expose them to alien microorganisms.

The original movie gave a shit about this stuff so I don't see why Prometheus gets a pass.

I've yet to see another movie held up to the same ridiculous scientific scrutiny as Prometheus

You don't pay much attention then as there are huge essays on how the destruction of the Death Star II would wipe out all life on Endor.

People have also written extensively about how the Xenomorphs biology is impossible.

Oh, I didn't know a degree in biology was required to enjoy the movie.

It isn't, but saying critics didn't criticize some of this bullshit means nothing if the critics lack the knowledge to grasp why it was wrong.

Did it "break your immersion"?

Literally the first sentence of my original post.

but not because of these dumb "He pet a snake, I'm waking out the theatre" reasons.

That was just one of the many examples of the characters not only acting abnormally, but acting against prior characterization.

If he hadn't previously shit himself about a dead Jockey it wouldn't have been galling. If it was a cute fuzzy bunny and not a dick-cobra it wouldn't have been galling.

But a guy who previously freaked out at a dead alien suddenly wanting to pet an alien snake just seemed chaotic-dumb.

If they had him acting in character and getting mouth raped after being ordered to attempt to capture it then it wouldn't have made me want to leave.