I don't think the risk to risk to the relationship between the NFL and College football lies in the NFL trying to get a bigger piece. I think there are two outcomes that could threaten things, and I have no idea if either of them will happen to any significant degree.
The first is the one I've already mentioned, the possibility that eligibility rules change to where enough of what would be mid-level NFL players decide they can make a career without going to the NFL and that both bleeds off and blocks enough of the talent pipeline that the NFL gets concerned.
The second is that as the super conferences emerge they end up monopolizing the media money. I think this has a high probability of happening. But the consequence of that could mean that the 2nd tier of what is now Div1 finds themselves in an untenable financial situation and they decide to drop out of the paid Varsity Sport system. That won't bother the super-conferences, but it will reduce the ratio between the number of paid tier college programs and the number of NFL teams. As above, this outcome would effectively reduce the size of the development pool for the NFL. Could it be enough the NFL would care? Who knows? I think in the end, for a school to survive it will either have to have a deep national tradition or big local media market it can have to itself. I don't know how many of those there are but I think the number is less than the current number FCS schools. Or the other way to look at it is that schools that are currently 'recievers' from their conferences instead of generators, will end up at risk as the other schools are going to want them out of their revenue stream.