A lot of the issue, I believe, is that those long-distance services cater to a lot of small towns that have no airport or good bus service. So Senators don't want to lose that service in their state. And they fight to keep the service, even if they are conservative.
However, successive directors of Amtrak have always opposed the discontinuation of long-distance routes. Congress could likely force the issue, but it's interesting that Amtrak leadership always leans in favor of them.
There are some routes in the northeast that Amtrak turns a profit on [1][2][3], and some others are subsidized by states enough to still make them worthwhile to operate (CA, IL, NC). But if the long-distance routes were defunded, they'd likely never come back under the Amtrak banner, and significant layoffs would ensue.
[1] https://news.ycombinator.com/item?id=15968720#15976146 [2] http://reasonrail.blogspot.com/2012/12/amtrak-routes-by-2012... [3] http://www.riarp.org/blog/2014/11/25/september-amtrak-report