I was pretty sure restaurant meals counted, and never had any problems, e.g. at the The Westin Verasa Napa my meal at La Toque was multiples of my night rate and posted without problems. I realise at some of the cheaper brands that isn't the case, but full service should be counted, except if for some reason the restaurant is operated by a third party, which is fairly rare. SPG used to not count transportation costs (I found that out once by mistake and was fairly annoyed), whereas Marriott (and as far as I am aware Bonvoy) does count such costs if charged to the room bill. Heck, at the moment in Asia you can earn Marriott points for eating in a Marriott hotel (including self pick-up) as long as you spend more than USD10.

My general view is that if it goes on your bill and it isn't going to a government or state then you should be earning. Then again, I always presumed resort fees earned points, can anyone find me a rationale why they wouldn't? This is from the Marriott website:
I do remember some places it mentioned you can't earn points on alcohol due to state law, so that may be one caveat that is fairly US specific.