I was on the Coast Starlight in February visiting from Denmark and had pretty much the same experience.
It started bad already at the bus terminal in San Francisco, where the guy in front of me got scolded for asking if the bus leaving was his bus. Maybe not the most intelligent question (it was rather well signed and announced), but he was nervous about missing his connection, and did not deserve a correction you would give a 5 year old. It wasn't even because the office was busy, with only me waiting in line.
Then boarding at Oakland I asked for a window seat. Here I got told - in a friendly manner though this time - that that is what everybody is asking for, and was assigned an aisle seat - in an almost completely empty car. I don't think at any point of the trip there was more than 5 people in the car and the other coaches were equally lightly travelled. I'm not really into that sort of "I have the power and you should know your place"-games. Instead I turned into a lounge lizzard...
Lunch in the diner was fine with busy but efficient and nice service and the food was fine too. I have no use for waiters running around disturbing my meal with pepper grinders and repeated "is everything fine", so that was good with me.
But again: I had asked for the latest available lunch slot, but only got 12.15, I think, and I headed for lunch well before I was really hungry. Still after I had had my lunch they kept announcing free slots on the last seatings, if anyone was interested. Again, what's the meaning of that? Probably seeing if they could cancel the last seatings on this lightly travelled train, but still annoying and poor service.
And it's not just the employees. After a short look at the cafe, management could really use to put themselves in the passengers position. It's not only the menu, but the cafe itself is murky and uninviting and does nothing to make anything on offer look the least bit tempting. The attendant seemed as tired as the interior but was friendly enough. I ended up just buying a beer (an exellent San Diego IPA) and eating when I got to LA instead.
Did this make it a bad trip? Not really, more like a meh trip. It could just have been much nicer and with measures that cost nothing or very little.