It's a core philosophy of coaches to let serviceable rookies play in front of veterans. No doubt the Seahawks saw enough from Wilson to let him start in front of Flynn. That doesn't mean Flynn was bad, or missed throws, it just means that Wilson showed enough to get a shot.
If you have two QBs in camp both playing well enough to win games, but one is a rookie you're gonna start the rookie. He could be a franchise player. You want him to get pro experience sooner rather than later. Seattle chose that route with Wilson and they were no doubt confident in their Defense to allow a rookie to start.
Matt Flynn was the odd man out in this equation. But I have no doubt he can play at a high level. If we see Terrell Pryor or Tyler Wilson get the start over Flynn it will be because they are exceedingly impressive in camp and pre-season (and that would be a good thing). It's a win-win-win QB situation in Oakland.