Try IMAP for Gmail -> Mail goodness
I use Gmail and Mail and love it, but use IMAP instead of POP. IMAP will keep your accounts synchronized so when you read a message in Mail it will be marked as read in the Gmail browser window, and vice-versa. I also use Mail on my iPhone and that works the same way. You can switch from POP to IMAP from Gmail's settings link.
If for some reason you want or need to use POP, I'd try going to your browser view of Gmail and marking all messages as unread, though I'm not sure that would even cause them to get pushed to Mail.