I think there are two separate sets of issues here.
One is Tom Brady getting involved in a business venture with a guy who has a history of trouble with creditors and the FTC. Guerrero is apparently clear of those troubles now. So, this is a personal and professional judgment by Brady that none of us really have the data to question on the facts. But, in my experience in the business world, "tigers don't change their stripes," so, if I were Brady's friend or advisor I'd probably have advised him not to do this. But, as I said, Guerrero is now in the clear and Brady has more data than I have...hopefully.
Two is the creation of a revenue stream related to team play or preparation for team play by an NFL team that financially benefits one of its players, beyond his salary. I'm virtually certain that there would be nothing, in the view of the NFLPA, in the CBA that would specifically prohibit this, as I assume Brady had this checked out by his lawyers and no doubt was smart enough to get an opinion in advance in writing from the NFLPA that this was kosher. However, there are two risks here.
The first is the possible appearance of impropriety. An objective or unfriendly observer might ask whether players are in any way informally pressured to avail themselves of these services to the financial benefit of one of their teammates. I think it would be useful to step back and imagine how we would be reacting if Peyton Manning had set up a business venture related to their play on the field that put cash in his pocket directly from his teammates.
The second is that we should be very careful how we read the quotes about and from the NFL in the article:
The article quotes the NFL as saying “We are aware of the arrangement and have not determined that there is any violation of the CBA...’’ That is a different statement from "We have thoroughly reviewed the arrangement and we have determined that there is no violation of the CBA." It just says that they have not, based on their awareness, determined that there is a violation. The statement does not close the door on the subject. If you're willing to "trust" the NFL on that, well, I live in Manhattan and have a very nice bridge in lower Manhattan connecting the island to Brooklyn that I can sell you at a great price!
The article also says (probably referring to the above quote, but providing more information) that "The NFL says it is aware of the arrangement and has taken no action, despite questions from some specialists in sports law and economics about whether teams should pay for services by for-profit companies owned by their active players and whether the relationship provides value to Brady that should be counted against the club’s salary cap." There is a big difference between "taking no action" and approving the arrangement. The quote also suggests that lawyers and economists have gone to the NFL with concerns over this arrangement.
I doubt we've heard the end of this.