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.