This is another of the recurrent dramas that we see play out based on the structure of rail transportation in this country. In the US (and Canada), outside of a few corridors (principally the NEC and its extensions), the rail network is in the hands of private railroads and exists to provide an avenue for freight transportation. In this context, passenger trains are, at best, an annoyance to the track owners. In much of the rest of the world (especially Europe), the rails are publicly or quasi-publicly owned, and their central purpose is passenger transportation; freight use is a very distant afterthought.
In order to improve the situation for passenger trains on the freight roads, the passenger forces (Amtrak, the states, the feds, whoever) have to make it "worth their while," at least to some extent. CSX says it is not "worth their while" to host more/faster trains on the Water Level Route. As Mr. Moore suggests, perhaps this is a negotiating ploy. While some of their positions have some legitimacy, though, they're undercut by the fact that other freight railroads (e.g., UP between Sacramento and San Jose) have figure out how to profitably co-exist with much higher volumes of passenger trains. CSX seems to be taking the position that there's just no way to make additional frequencies and higher speeds work. I'd be surprised if that were true. And if CSX continues to adhere to that position, they could be in for a lot of unpleasant scrutiny (passenger-related and otherwise).