It seems that Philbin and Sherman would rather role the dice on a young Qb through the draft then risk a couple years with Flynn.
Flynn may never amount to a true top flight Qb, but with enough talent around may win you 10 - 11 games per year. You get a franchise guy, the talent around need not be as superb to net you 10 - 11 wins a year. Hence the gamble on a younger guy, reward far outweighs the risk. Always will.
If anything, Philbin + Sherman will be given 3 - 4 years to find and develop a young franchise quarterback. That's what they were hired to do, and that's what they'll be devoting their entire resources to.