I have seen many comments on different blogs and forums where English native speakers spelled you're as your. I'm not a native speaker, but I know and understand the difference between the two. Why is there a confusion?
My initial guess is that your and you're have similar pronunciation and because I carry some accent from my native language (Romanian) I can identify the difference better.
Edit (thanks Chris): The same can be asked for other homophones: there/their/they're, its/it's.
Best Answer
The answer is simple.
You just need to think about how you learned your native language. By ear.
Children learn how to speak their native tongue first, and only then learned the grammar and spelling. Thus, many will "sound" a word out to spell it.
English language learners, on the other hand, usually learned how to spell a word first, and focused on pronunciation later.