I was also under the impression that freight trains had priority, so I looked and found this article:

http://www.sfgate.com/opinion/article/Amtrak-has-priority-ov...

I've experienced these delays many times riding the California Zephyr, and the conductors always say something about the freight trains having priority. According to the article this is because Amtrak is persistently ceding priority, despite federal regulations prioritizing passenger trains.

edit: According to the WaPo article linked by jey in this thread, this ended up overturned in federal court, so I guess as of 2017, freight does have priority over passenger trains in the U.S.