I would not be surprised if the RPA is a far left organization; so I wouldn't worry about it. They are just fear mongering over nothing.
I can say with reasonable certainty that, among other things, at least two board members are Republicans in their "normal lives". I know we've also got a few Democrats on the Board as well (and a bunch whose affiliations and alignments I'm not clear on). And I will say that there have been one or two times where a few of us have had to call individuals out for being improperly partisan in a non-partisan organization, but you're going to end up with that in almost any 501(c)(3) organization involved in advocacy.
Some of this is, in all fairness, standard operating procedure for any non-profit ("never waste a crisis" is a mantra that cuts across party lines; I have yet to see an organization tell its members to sit back and relax much as I've never heard a politician declare a given election to be unimportant). They'd be making the same noises if a Democrat tried the same thing, and to be frank the management would not be doing their job if they didn't pursue the potential revenue from a given crisis situation. Any leanings on the political spectrum are going to come down to where the parties fall on this front on a given day.
This isn't to say that I'm not occasionally exhausted by the perpetual "crisis mode" that we get stuck in, and the fact that a lot of the shots are coming from a given angle is frustrating. It has gotten old, and gotten old fast.
As to the situation between the parties, while it is true that the Democrats put a good deal of money into passenger rail, an outsized portion of that went to California. Granted, this was not for a lack of first-round distributions to other states, but some of that money was doomed by the fact that the Obama administration held back on the grants in an attempt to use them as election goodies in the 2010 midterms rather than working to lock down contracts before the elections. Perhaps more frustrating is that while a good deal of money went to various state corridors, the national network came up very short on attention. Again, this wasn't entirely the administration's fault (who would have thought we would
still be waiting on those CAF sleepers, as well as the N-S order fiasco?) but the carve-outs on the stimulus grant were problematic and Amtrak didn't get the replacement equipment it needed then (and still needs now) even in what should nominally have been one the most favorable of environments in recent history. I'll grant that we'll never know what follow-up budget packages in 2011 and 2012 might have looked like, but it would likely have been more of the same.