People who are good spellers have strong visual memories for how words are supposed to look. A little bit of knowledge about the linguistic roots of words helps, but mostly it's about how the shapes of the letters look together. This is why, when I was uncertain about spelling (long long LONG before spell check), I would write the two (or three ) spellings side by side, and go with my visual gut.
I started making a lot of mistakes, however, as I spent years reading misspelled student writing, and now, of course, all the misspelled words on the internet. Having seen them WRONG so many times, I had difficulty remembering the correct spelling.
If you don't have a good visual memory, you will misspell a lot of words. Especially words that violate general rules.
It's as simple as that.