That's because Franklin's strength is in the areas specific to college football: recruiting, program building, working with young people, among others. He's not a great X's and O's guy. O'Brien was great with offensive tactics (though his teams didn't have great defenses), but he was not good at the college football stuff.
It is rare for college football coaching skills to translate to the NFL. The best positive example I can think of is Jimmy Johnson who was a workaholic, a fantastic evaluator of talent (which helped him build a solid Cowboys D even though most of the stars of the team were offenses), and had an ability to discipline professional athletes.
I don't know what Schiano's strengths are as a coach, except he has enough tactical acumen to do more with less, and is developing a culture at Rutgers. Not bad at all, but I don't think he's light years ahead of Franklin.