I'm not sure this is as bad of an idea as many people in here are making it out to be. In fact, I think it's probably the smart thing to do for the following reasons:
1) He's only been a college starter 2 years. He probably doesn't think he's ready for the pros yet - and if he does think that, he's probably right.
2) Assuming there is a rookie cap (or slotted system) in the new CBA, that would take place immediately, not starting in 2012. There's no pot of gold waiting for him in 2011 that he would be walking away from.
3) Next year in the NFL is entirely up in the air. Now I don't think for a second that there is going to be "no football" at all. I have no doubt we will see football in 2011. But we might lose training camp and we might lose some of the preseason. It could be a recipe for disaster for any rookie QB banished to limbo unable to prepare. The entire year could be a complete waste. He's much better off playing a full season at Stanford than doing nothing at all until late August, followed up by a couple months of riding the pine.