It would seem that worry extends only so far. In this case, if what you're saying is accurate, Comcast intends to take (i.e., extract rent), and it just doesn't want to get noticed while it takes. Fear of the FCC and potential consumer backlash do not extend so far as to help it to reconsider its basic strategy of expanding rents, even as its merger with Time Warner is under review. There's a certain boldness to Comcast's move in working out this deal with Netflix.
ISPs have the option of making content providers(Netflix), or content consumers(you and me) pay more. They're choosing content providers because they don't want to make net neutrality more salient for their customers.
Netflix isn't just going to absorb those payments, they'll have to pass them along to customers. Customers will want some explanation for why their bill is going up . And if Netflix's per-user costs become substantially different at different ISPs, they'll have to start thinking about ISP-specific surcharges...
Comcast worries about the FCC and Congress, not its competitors.