Most rural areas do not have bus service available, and even in larger areas (think cities with up to 100,000 people), bus services are quite limited. Outside of large cities the US simply does not have the same culture regarding public transportation that you find in much of the world. Also, although sometimes it is wasteful, in areas that support multiple schools (think elementary, middle, and high school), starting times are already staggered so that the same buses might pick up high school students first, then middle school students, and finally elementary school students, and have similar routes for taking them home. So while there's certainly downtime, it's not quite as bad as it might sound. Finally, I believe - though I might be wrong - that school buses have different safety standards than other buses, which could cause problems for districts that were to try and push the students to city/county bus services.
Regarding security, I can use the high school I went to as an example. When I went there, it was a very open campus, and fences were only used around the athletics fields, and were more to stop balls from heading into the street. During expansions and renovations, however, they built additional buildings around the edges of campus to act as barriers, and added more fencing, leaving only about 3 entrances to the grounds that were more easily monitored. This was despite the fact that it was a very safe area with low crime. I personally don't like it, but I suppose it's an easy way for schools to show that they're trying to make it harder for things to happen.