It's been said before, but the your/you're barrier is definitely my biggest peeve, with the their/there/they're barrier a close second. I used to teach college composition; I gave the kids an actual, factual
cheat sheet and they still screwed it up. Seeing someone misuse those automatically takes my first impression down a notch.
I'm not blameless, though. I frequently misspell words by getting the vowels wrong--spelling "sentence" as "sentance" or "believe" as "beleive." Whoever mentioned native speakers learning phonetically was, I think, right on the money--the words I screwspell would sound the same with the wrong vowels.
(I hope portmanteaus like "screwspell" aren't anyone's pet peeves

)
Jam it back in, in the dark.