There's a lot of reasons, as many as there are special interests in Marin Co. Chiefly, though, Novato is attempting to stifle any furthur development -- in fact any change at all-- that would impact the current "look", "feel" and demographics of Marin, and their town in particular. Right now, the railroad, whether it's NWP freight trains or SMART commuter trains or both, is an element that could, in their minds, effect "negative change" to the area. So it's being fought...
Whether reopening the NWP will truly be an economic boon to the North Coast has yet to be seen, but either way, The North Coast is of no concern to Novato and Marin. Similar attitude was proven when the first SMART initiative failed last year, most strongly opposed by Marin voters, especially northern Marin. SMART would have been (well, will be, it's inevitable and Novato can't push back that long)great for the greater North Bay and Sonoma (which overwhelmingly voted for it), but again that was of no concern to Marinites.
"Me and mine, first, foremost and only" is the Marin way.