League average rush EPA is negative because most teams don’t use the run game properly.
Historically there was the idea that you need to “run to set up the pass.” Smart teams now know that it’s basically the total opposite.
There’s also the idea of “3rd and manageable” where teams opt to run the ball on 2nd and 10 because they want to avoid 3rd and long. Again, running the ball on 2nd and long is a very negative EPA play, yet even today some teams still do it religiously, which tends to drag down the average.
It’s not that teams should abandon the run entirely. It’s that the run game should largely be used situationally (i.e short yardage and clock-chewing situations) as opposed to being the staple of a modern offense. Multiple teams every year still have positive EPA/rush. Even the most pro-pass, analytics-based people aren’t going to argue a team like Philly or Baltimore should abandon the run.