It's impossible to do a tournament of 48 teams using head-to-head as primary factor. A beat B, B beat C, C beat A.
A team with a 40+ RPI is not going to be a top 16 seed. The coach needs to schedule better, especially playing in the B1G, if he wants that.
These tournaments are set up from the perspective of the higher-regarded teams. Think of the 8-9 matchup in the NCAA basketball tournament. The 10th seed is more favorable than both, because a win doesn't mean facing the #1 seed in the next round. So it's unfair to the more highly regarded (8, 9) teams. But it's impossible to balance everything out for every team from top to bottom...
Rutgers will be fine. MD Myers is going to score no matter who or where they are playing.