One of the issues around net neutrality is whether you are creating different rates or charges for different content providers. That's the big controversy here. So you have big, wealthy media companies who might be willing to pay more and also charge more for spectrum, more bandwidth on the Internet so they can stream movies faster. I personally, the position of my administration, as well as a lot of the companies here, is that you don’t want to start getting a differentiation in how accessible the Internet is to different users. You want to leave it open so the next Google and the next Facebook can succeed.
What Obama seems to be opposing is the idea of paid prioritization, or the notion that companies should be able to pay for better, smoother access to consumers. The remarks also seem to contrast with the FCC's current proposal on net neutrality, which would tacitly allow for such commercial deals so long as the agency didn't consider them "commercially unreasonable."
On the other hand, FCC chairman Tom Wheeler has on occasion come out explicitly against Internet fast lanes, saying that paid prioritization in his view would be commercially unreasonable.
While the friction isn't immediately obvious in the response, Obama may just have let slip some frustration.