There's multiple factors contributing to the lack of success in the running game. Yes, the lack of respect to the passing game is a big part. Even if a defense isn't bringing safeties into the box, do you know how much easier it is as a DB when you know the offense is only comfortable running three or four different routes? It makes keying on the running back a lot easier when you don't have to worry about a receiver getting behind you. If I'm a Defensive coordinator, I'm asking my safeties to key on the run and underneath stuff and I'm taking my chances with Rosier throwing it downfield against man coverage every time.
Now, I'm not letting the O-line or Searles off the hook either. In two years the offensive line has been below average in run blocking and pass protection. I understand that linemen often take the longest to develop and you rarely see dominant freshman or sophomore offensive linemen. However, going into year three, they've got to show some kind of improvement. These younger guys have been in the system for a couple of years and need to at least be marginally better. There's no excuse for the goal line and short yardage struggles against a majority of the teams we've faced.
Now, let's look at it realistically. Outside of 2000-2002, Miami has NEVER been known for dominant offensive line play. Part of what made Howard so special was his switch in offensive philosophy away from an option/power running style that most college teams favored at the time to a quarterback-centric, pro style passing offense. It only makes sense. Florida is hardly known for producing power blocking linemen. If you watch high school football in south Florida, you won't see teams lining up in an I formation and running the ball. The talent here is at the skill positions. You see a ton of spread with QBs making quick reads and short throws against defenses that are spread out trying to defend a multitude of receivers. Bringing in all these south Florida kids and putting them in a power running offense is shooting yourself in the foot.
It's incredibly tough in today's college football to assemble a totally dominant offensive line that can just bully other teams. Even Alabama had to make a switch to a more dynamic passing QB in the championship game because they couldn't just line up against Georgia and run it at them. So even a team with nothing but 5 star, NFL ready linemen needed to rely on their quarterback to make plays in their biggest game of the year.