I suspect this is historical. As I understand it, the original intent was that submissions would be ranked by their upvotes, and that only items that were inappropriate should be flagged. Then sufficient flagging resulted in deletion.

Comments, on the other hand, couldn't be deleted by flagging, but simply got ranked according to their votes.

PG has decided to count flags as downvotes. He continues to tinker to try to find a good balance of these limited controls. As the site grows so its focus is getting lost, and these changes are an attempt to keep things "on track."

That's my understanding. It's probably wrong in detail, but it feels right in general.