Even if their coaches were complicit, the "school" would still be the victim, as that is where the money is coming from and who is being defrauded.
I don't know how the voodoo accounting methodology of these shoe companies is being used to hide what's really going on, but it seems to me that the only way the schools could be getting dinged for the cash payments is if they were getting deducted from the school's monthly contractual payments from their shoe company. To me, that would leave a reasonably easy to follow paper trail, so it wouldn't make a whole lot of sense to do it that way.
I see it more as the schools knowingly participating in the whole deal, while using the shoe companies as sort of agents, creating a layer or buffer between them and the recruits/families. Under those circumstances, calling the schools "victims" is disingenuous at best.
I think the FBI sees it as quantifiable that schools will suffer some economic loss if they are found to have violated NCAA rules. Sanctions, loss of scholarships, postseason bans could all negatively affect the schools' bottom line. That's what makes them "victims", although those potential losses are difficult to quantify, and likely self-inflicted to a greater or lesser extent, depending on how much was known by school administrators and staff about what was going on.
The folks making theses deals apparently thought this was a win-win-win for everybody as long as the feds weren't involved. The schools were getting players they wanted, the shoe companies were signing players to be loyal to their brand after their college careers, and the intermediaries, including coaches and others, were making money off the deals. Everybody wins, until the FBI tears it all down.