Without going back and looking it up, the NCAA really focused upon the "sponsor" from the YMCA who coordinated that program being an SU booster, and also that there was some alleged impropriety [ebezzling? Again, not looking it up] from that individual that didn't have anything to do with SU or our players, but which cast suspicion on him being of questionable character.
In and of itself, getting paid to ref is not a big deal -- the NCAA suggested that the pay was too "high," but it wasn't a very large amount of money, and this wasn't a no-show situation. IIRC, the NCAA "issue" -- which was very minor -- was that the players got college credit for the internship with the YMCA, but their hours weren't properly documented, which meant that the amount of time they put in couldn't be verified.
So, all of those things in conjunction made the NCAA write it up in a salacious manner, alluding to the fact that there was "smoke," so there must be a fire.