Nemo may be able to order his crew around, but he can't control all living things… even if he really, really wants to. In 20,000 Leagues Under the Sea, Nemo's underwater dominance does not go uncontested. And when certain forces of nature get in Nemo's way—giant squid, blocks of ice, huge whirlpools, certain species of whales that seem to unjustly "oppress" other whales (yeah, this guy is actually way crazy)—he's not shy about vanquishing them. So, yeah, the captain fancies himself a freedom-fighter. But he doesn't take kindly to other people breaking his rules. Kind of hypocritical, don'tchya think?
Nemo is the ultimate symbol of self-reliance, a great example of a man totally in harmony with the world around him.
It's no coincidence that the Nautilus gets stuck right after traveling to the South Pole. As Ned says, "You always have to stop when [Nature] has laid down her limits" (2.13.30). The group escapes that time, but when Nemo drifts toward the Maelstrom, he finds himself pitted against the very outer bounds of Nature… and he might've lost that fight.