I think the bed icon clearly demonstrates what you use a hotel for - a place to sleep. This encompasses hotels that aren't several stories tall as well.
However, outside the context of other reservation-related icons, I agree that the "building" icon is lacking in specificity. The bed icon is slightly better, but still by no means good. It could just as easily mean sleeptime or rest, as opposed to daytime or work.
It's a shame there are no symbols or architecture inherently associated with hotels. Maybe that's why they tend to feel so anonymous and devoid of any soul...
The distinction here is that you don't get in an airplane to sit in the seats, you get in an airplane so it can fly somewhere with you in it, and the shape of an airplane is very good at conveying that. With a hotel, I don't go there so I can admire the building, I go there so I have somewhere to sleep.
And no, I have no idea why flight plus hotel equals desert island with palm trees...