No concern at all. I've parked outside a couple hundred hotel/motels across the country.
I do try to stay in a decent part of town, in a place with a well lit parking lot, and I prefer to stay in a place where I can park right outside the room, if possible.
Other than that, keep the insurance paid up and lock the forks, is all I've ever done.
What JayKS says exactly. One more level of security is brake disc lock for the front wheel, just please, please, please remember to remove it in the morning, seen a few that didn't and it wasn't pretty.
I prefer to pre-book my hotels/motels so I stay where I want to stay, not where I have to stay. Use google maps to check out locations before hand and "see" what else is in the area; a little bit of research ahead of time can save a lot of heartache later.. Take all your overnight stuff you will need out of the bike and take it to your room. Lock up the bike, cover if you feel the need to.
There are others that really like the "freedom" of a motorcycle trip and pick their hotels at random each and every night of their trip. Someday I will have that courage and wanderlust to travel that way but presently I am usually on a tight schedule (itinerary by the minute) and must adhere to my travel plan as closely as possible.
Don't worry about the little towns, worry about the hotel next to the truck stop beside the interstate, way more people with the right tools and equipment going by there looking for opportunity. I find small town America far better "protected" if you get my gist. Pick a chain hotel when you can. There security camera system is usually better but I've gotten great service with Mom n Pop places as well that have put our bikes under their watchful eye all night long.
Avoid parking too close to automatic doors at the front of the hotel, they can mess with the HD fob security system. Park close by not right beside them. Some hotels offer bike parking right near the front. Some Best Westerns have a deal with HD and H.O.G. for better rates and provide a bike wash area.
Mostly, relax, get some sleep. Your motorcycle and it's contents can be replaced, you on the other hand are a one of kind broke the mold kind of guy that many folks are just aching to meet and swap lies with. Arrive fresh, and ready to have a ton of fun for the week.