Hotmetal welcome to the board. As for your question............I do a lot of overnite trips and stay in anything from Motel 6 all the way up to Radisson or Hiltons. I have traveled all across this country, back and forth, up and down, western Canada and Mexico.
The measures I take: I try to always get a street level room with parking in front of the room (but that's not always possible). If I get back to the motel late and all the close parking spaces are taken, I'm not above putting it directly on the sidewalk.
I have my bike programmed where the alarm sets itself thirty seconds after I turn it off. Sometimes that's a nuscience (like when I'm putting gas in it and I'm still sitting on it) but the protection that it provides me (when I'm running into the store, or into a friends for a second or anywhere, where I do not normally mess with locking it.
Besides making it as visable to my room as possible and the factory alarm, I lock the ignition (which pops real easy with a pipe wrench, so it's only a deterant and not a real lock) and I use a disc lock (it keeps the bike from being wheeled away and can not be cut off.
Other than that, the best protection I have is my insurance and that's why I have it. For that reason, I do not loose any sleep worrying about my bike. On insurance, I might suggest that you get insurance that covers it for full replacement rather than insurance that will just pay off the loan.
I rarely use a cover, on long trips. I just don't have room for it and never seemed to use it the few times I did take one. Use YOUR best judgement and damn good insurance and enjoy the ride and get your sleep! [smiley=xyxthumbs.gif]