In California, Amtrak established many connecting bus routes where there had been no recent train service, but that was done with considerable support from the California Department of Transportation; I imagine local support in any given area would have a lot to do with what bus routes were established.
Sometimes it seems to have to do with the providers Amtrak chooses for Thruway service. In the upper Midwest, Amtrak often works with Jefferson Lines and overlays their service on the existing Jefferson Trailways service, but it looks like you can only interline by buying through Amtrak.
There are a few surprising omissions - there's no Thruway service to:
-Des Moines from Ottumwa (I could have sworn there was)
-Chattanooga from Atlanta, or anywhere within Georgia for that matter
-Huntington, WV from either Pittsburgh or Charleston, WV
-Phoenix from Maricopa (but there is a Thruway from Flagstaff, ironically)
-Asheville from High Point via Winston-Salem (which does have a Thruway)
-the Branson, MO cluster from Kansas City, MO
-nearly anywhere in the NY Southern Tier, except Jamestown to Buffalo.
I was quite surprised to see extensive Thruway service in Wyoming though, as well as lower Michigan, Idaho and western Oregon, and the North Carolina coast.