Is colo space at the ISP an unlimited resource? If not, then it will end up priced out of the reach of the small guys.
I suppose the ISP could offer some kind of "virtual colo", where instead of putting your servers in the ISP data center for fast access they offer some kind of faster connection to your data center. This would have two big advantages over physical colo. First, it would not have the space limitations so it could be more widely available. Second, the price could be based on how many customers you are serving at the ISP so that even small content providers can afford it.
This now sounds similar to "fast lanes", which have been the major focus of opposition to the proposed approach to net neutrality of trying to regulate under section 706.
The problem I see is that in both the company specific CDN approach and the "fast lane" approach it comes down to a content provider is making an arrangement with an ISP to make that content provider's content better for its customers on that ISP.
Is that against net neutrality? If the answer is "yes", then I don't see why it should matter if it is done via physical boxes placed on the ISP's network or by prioritizing traffic from that content provider or by purchasing a higher capacity interconnect to the backbone providers that content provider's traffic comes through. This seems to me to be one of those things where it should be looked at as a black box, and net neutrality should be concerned with the externally visible behavior of the box, not the mechanisms within the box.