I park outside, but my company has a parking ramp and the bike is "sort-of" covered. It is under the 2nd deck of the ramp, but if the wind is blowing at all my bike is still exposed. Anyway, in answer to your first question, I don't ride a beater, I ride a nice cyclocross bike. I lock it with 2 types of locks, and fortunately my office is in a "safer" area and the bike rack is cemented into the ground right at the front door of the parking ramp, and within view of the security cameras. I have even forgotten to remove my saddle-bag a few times and not had anything disappear.

For Bad weather...clean your bike. That's really all it takes. If you ride in rain/snow, wipe it down. I buy the cheap shop-towels at walmart for this purpose. Also, clean/lube your chain frequently and get/use fenders.

On the route issue, get used to riding in the road. If you are traveling at any speed (10 mph + ) you are safer on the road anyway since drivers don't expect things on the sidewalk to be moving that fast. Try riding the route on the weekend to see how comfortable you are with lighter traffic. If it won't work, try to find a route via side streets. Best of luck!