score:9
You've identified most of the standard options. Almost all travel between Denver and Fort Collins is by private car (as is almost all travel in general in the U.S., outside of a handful of corridors between large cities), and relatively few people are expected to take Amtrak to Denver in order to get to Fort Collins, so the schedules are not coordinated.
You could spend the night in Denver, then hop on a Greyhound in the morning. LoDo has plenty of bars and restaurants to keep you entertained.
There is no getting around the fact that the airport is very, very far from downtown and out of the way for getting to Ft. Collins. But you can take a taxi from downtown Denver to the airport for about $55-60 rather than wait for the FX bus to amble along, which might enable you to catch an earlier shuttle.
Besides SuperShuttle, there is a competing service called Green Ride Colorado which travels between the airport and Fort Collins. They have better Yelp reviews than SuperShuttle, for what that's worth.
I see about four private car services that come up on a web search for Denver airport transportation from Fort Collins (but you wouldn't need to take them to or from the airport). While it wouldn't be cheap, you could probably negotiate a rate cheaper than the taxi.
You could post on Zimride or another rideshare service to see if anyone else is heading from downtown Denver to Fort Collins in your time frame. Of course, depending on a stranger entails its own risks.
You'll arrive too late to rent a car, as there are no facilities at the Amtrak stop (as you are probably already aware, Denver Union Station is undergoing a massive renovation, so the train stops several blocks away), and the neighborhood rental car locations will be closed by the time you arrive. You'd have to get to the airport to rent a car, and once you've gone that far, you might as well just take the shuttle. But if anyone arriving earlier happens upon this thread, it's an option to consider.
Upvote:9
There is a public commuter bus service running between Denver and Fort Collins: Bustang North Line. It runs from Denver's Union Station (which is where Amtrak stops) to the Fort Collins downtown transit center, with only two intermediate stops (I-25 at US-34 in Loveland, and the Harmony Transfer Center at I-25 and Harmony Road in Fort Collins).
The bus runs mainly during commute hours, with just a few buses on weekends. As of this writing, the last northbound service departs Union Station at 7:00 PM on weekdays or 7:30 PM on Sundays. Since Amtrak long-distance trains are often late, you'd want to have a backup plan, but this could be a convenient and economical option if you arrive on time.
The fare from Denver to Fort Collins is $10. The bus has a large luggage compartment underneath, and free WiFi.