*** This review may contain spoilers ***

For people who don't get it, here are some possible interpretations –

The cowboy is rounding up lost souls. That's what John Person (Jon Favreau) is at the start of the film and that's what Ruthie (Rachel Leigh Cook) is at the end. In fact, Ruthie is even more lost than John which is why she goes and he doesn't.

The suitcase has size 11 shoes, obviously not meant for Ruthie but for John. At the film's end when John is bowling we see his size 11 bowling shoes, confirming that the suitcase was meant for him.

The suitcase is what all lost souls carry. It's what the dozen lost souls at the end carry.

Neely (Bud Cort) works for the aliens and he does the research on who is lost and who isn't. That's why he has a dossier on John.

Dan (Brent Briscoe) warns John that the aliens take people's sperm through their neck. Near the end of the film John has a bandage on his neck, and in his final appearance we see that the FBI agent (Kelsey Grammar) also has the bandage.

The point of the film is that life is short and worth living and you shouldn't waste it. Ruthie tells this to John and John tells it to Ruthie.

Through the experience John finds meaning in life through his relationship to Grace (Joey Lauren Adams), and once he does this, his life takes a turn. He's now got a job as a second lead and he can throw strikes.

You may or may not like the film, but it's not that hard to understand the symbolism.