> So the government very well can be against 49%

I think you're confused.

First, it is not always the case that there are only two parties. You can totally have a government made by representants of all "relevant" parties (by "relevant" I mean that the party needs a minimum size, otherwise anyone could create a party of one person).

Second, your ship example is pretty weird. The people gets to elect representatives regularly. It's not embarking on a ship with complete strangers: you have been on this ship all your life. "Never have been on a ship" would mean electing a newborn baby... that wouldn't count as a functioning democracy :-).