"It does not appear, given the prior awareness of MU staffers, that the housing and use of a vehicle would have been considered impermissible benefits by themselves. But it seems they became viewed that way after the NCAA and school in their review determined that the players had been compensated “for work-not-performed at a business through a summer internship program,” as stated in Missouri’s release."
http://www.columbiatribune.com/sports/mu_basketball/banned-missouri-booster-says-he-meant-no-harm/article_6c7158b1-5102-58fe-bdb1-c06c36aeacc1.html
They only became impermissible benefits after the fact when MU and the compliance department changed their stance on the internships. At the time they were given, they were just approved parts of participating in the internship.