By definition, a trademark is being used in commerce. To get a federally-registered trademark, the applicant must submit an affidavit of use stating that the mark is being used in commerce. An affidavit is subject to the penalty of perjury. If you submit an affidavit that you know is not true, you can be punished by up to five years in prison.
Use in commerce of a trademark entails making money from it. This is inapposite with the NCAA's principle of amateurism. Any college athlete with a federally-registered trademark admits to breaking NCAA rules. This can be easily alleviated by first filing an intent-to-use application and later filing an affidavit of use once the athlete is done playing college sports. This is not what Manziel did. He filed for a trademark on the Principal Register, and submitted an affidavit stating that "Johnny Football" is being used in commerce.
Apparently, the NCAA did not allow Manziel to obtain a federal registration, but just to protect his common law trademark rights until he could use the Johnny Football mark in commerce after he was done playing football at Texas A&M. Protecting common law trademark rights does not entail submitting an affidavit saying you are using a trademark in commerce. As it is, Manziel either committed a fraud on the United States Patent and Trademark Office by submitting the affidavit, or is admitting to breaking NCAA rules in submitting the same affidavit. The only other conceivable explanation is that the NCAA is allowing Manziel to play by a different set of rules than anyone else, by letting him have his trademark and play football too.