If Alex Smith has proven that he can't get to the SB with the most complete team in the NFL around him why would any other team think Smith can win with them? Flynn has a higher ceiling because he could very well be better than Smith. In other words Flynn hasn't proved that he can't.
Seems like the JS philosophy of drafting so far is primarily O-line & D-line in the first round except when we had that second 1st round pick we used on Earl Thomas. Looks like they are pretty good at finding everything else we need in later rounds.