I thought he'd get a mulligan for having several very good years, as well as last season's CFP semifinal appearance. That, plus there was still plenty of time to turn the team around and get them to a bowl game.
Normally, starting out a season 3-3 isn't going to get you fired, but I'm guessing that because he back to back games where PSU was favored by 3+ scores, their Board of Trustees panicked.
His pattern of success was very good, but not elite. If anything, his record looks a lot like Brian Kelly's, maybe even a bit better.
You're very much correct, that he can rebuild a program and get it to top 10 contention. While a lot of the credit for his initial success goes to Bill O'Brien, Franklin still brought in good recruiting, and developed a lot of NFL talent.
He blasted away the weaklings, comfortably beat the average teams, and usually beat the good teams, but when it came to the very good or elite teams, he didn't exactly have the best of success.
2-3 loss seasons became the norm over there, though.