I've been staying at hotels since the 1970s (and earlier, when traveling with my parents.) In nearly every place, in every price-point where I've stayed, the bathrooms were as good as they are today. That is, all hotels in the US that I have stayed in, the bathrooms were en-suite, they were clean, and the sanitary plumbing worked fine. (OK, one place in Watkins Glen NY where we stayed had a water main break, not the hotel's fault, and the toilets wouldn't work, but we were leaving that morning anyway.) I had two experiences where there wasn't hot water in the shower. I stayed in a place in London, UK with a shared bath and toilets. While not as convenient, these were well maintained and perfectly clean, and standing in line in the morning to take a shower was a pleasant social activity.
With regard to Amtrak, while I have seen some incredibly clean restrooms in coach on overnight trips (a ride on the Silver Star in 2012 comes to mind), they really have a problem keeping those public restrooms clean on long trips with high load factors. I particularly remember (and not fondly) a ride on the Vermonter, which was standing room only between White River Junction and New Haven, and still pretty crowded all the way into New York. After we left New York, the odor from the restroom wafted to our seats at practically the other end of the car. However, in the sleepers, I've never had any problems with foul restrooms, even the upper-level ones in the Superliners. I also have no problem with the in-roomette toilet in the Viewliner I's if I'm traveling by myself. I always sleep in the upper bunk, anyway, and it's kind of convenient to just climb down and deal with a call of nature, instead of having to get dressed to go down the hall. On the other hand, if I'm sharing the roomette, it's a pain, I either have to shoo my partner into the hall while I do my thing, or head down to the coaches. I balance, I'll be looking forward to having a puplic restroom in the sleepers the next time I ride a Viewliner 2 sleeper. The one time I rode in a bedroom, I was fine with the en-suite shower-toilet combo, though you have to be careful to make sure it drains completely inside the bathroom, and you need to keep the cover over the toilet paper roll completely closed when you take a shower. In any event, I don't think that any of these options are particularly risky in terms of transmitting respiratory viruses. However, it would be helpful if Amtrak pair more consistent attention of en-route cleaning of all toilets.