There are two key points here:
- Your deck starts out bad.
- Many cards are much better in the early game than later.
You can use upgrade to solve both problems. Getting rid of your starting copper (and likely estates) will improve your deck. So will trashing that first-turn buy that's just too weak to get you to provinces later. It's a non-terminal action, so it gives you a way to trash these cards without wasting turns, as you tend to do with something like chapel or steward. And do remember: it's an upgrade. You're not just removing a weak link, you're replacing it with something to strengthen your deck.
There are some great special cases, too, like upgrading four-cost actions to duchies in the end game, and trashing curses.