There are hundreds if not thousands of great movies. If one movie doesn't make some arbitrary list, it doesn't mean it's hated.
I do think there are some reasons that work against The Shawshank Redemption that aren't unreasonable.
1. Frank Darabont isn't considered any kind of significant auteur based on his body of work and critics tend to conform to auteur theory to one extent or another.
2. I don't think the prison movie (or Stephen King adaptations) is a significant enough genre that it needs to be represented in some list. It's not part of some larger movement like the French New Wave or German Expressionism either where a vote for it draws attention to the movement as well. The Shawshank Redemption represents The Shawshank Redemption alone.
3. The Shawshank Redemption isn't innovative in any way. It doesn't really have influence either. Casablanca isn't really innovative either, although it has some added war time resonance, but nobody points to The Shawshank Redemption and says "this new film is clearly possible because The Shawshank Redemption showed the way."
4. The Shawshank Redemption is really a home video / cable success story rather than a cinematic success story. It's small in scope as well. Nobody really talks about a retrospective run or includes it as part of film festivals. The conversation about it is elsewhere than where you find critics.
5. There really isn't that much critical discussion of the film. It works like gangbusters emotionally, but is anyone writing papers on the hidden symbolism and workings of the film? I don't think there's ever going to be a Room 237 about The Shawshank Redemption.
6. Tim Robbins and Morgan Freeman are good actors, but they're not cinematic icons. There's not much study of their filmographies.