A decent proportion of the population frequently run internal monologues in the voiced manner - when I'm typing this out I can hear (not actually hear but mentally hear) someone speaking the words as I type. I assume the frequency of homophone typos are due primarily to this - since both skew and SKU are identical in my inner monologue and I'm trusting my fingers to choose the right combination.
I think homophone spelling errors are a different issue though - english education in the US is really quite poor so a lot of grammatical rules[1] (they're/their/there) and spelling aren't really well impressed on society at large - people will hear a term in conversation and start using it in their own speech, when they arrive at typing it out they'll make their best guess at spelling and it'll probably end up a roll of the dice which homophone their spell-check ends up shoveling them towards.
1. /me types while admitting they constantly type in spoken english - preferring the spoken sentence construction rules. Something something glass houses and stones.