Having a flexible airfare with your Chicago connection was good planning. Mega-late long distance trains happen.

Once you're home, it would not hurt to call Amtrak, ask for Customer Service, and see if they might give you something for your expenses and trouble. It would be in the form of a voucher toward future travel. They don't have to, so they might say no, but Amtrak tends to be reasonably fair with these sort of issues, so it would not hurt to ask. The delay with your train was an Amtrak issue (locomotive failure), so they might be willing to provide some good will.