No, a story does not need a villain.
There are many stories in which a person struggles against nature, struggles to survive, struggles to invent something new, etc.
All the story requires (to be interesting) is a person trying to do something that they do not find easy, so they have setbacks, make mistakes, or have to sacrifice to make something happen.
In writing, it can be easier to do this if another person is opposed, because the plausibility of difficulty is not questioned; this other guy is shooting at them (figuratively or literally).
But look at the movie "Juno" for example; a teen girl gets pregnant and has to decide what to do. There are no villains, her parents are supportive, she has to tell the father (her friend), decide whether to get an abortion or have the child, then whether to keep the child or put it up for adoption, then choose an adoptive parent. No person harshly opposed her at any time (though opinions were expressed about abortion).
In Castaway, Tom Hanks is stranded by accident on a deserted island, and must figure out how to get home. Again, no villains. Consequences of being gone and presumed dead for years, but nobody trying to thwart him.
You have a perfectly good story with a crew against the elements, but it sounds to me like you have let them solve too many problems by "settling in" to their situation. In this type of story, they cannot settle until they have everything they want, or know they are permanently denied what they want; and there the story ends.
You need to find that wrong turn. Kick that environment into a higher gear of opposition, with dangerous predators, heat, cold, starvation, illness, hurricanes, earthquakes, vipers, whatever. This doesn't get easier, every skill they gain for survival gets offset by nature throwing another bucket load of crap on them, trying a fun new way to kill them.
Or they come to an impasse, a bridge is out, or there is no bridge but the river is too fast, and they have to backtrack or find a way around it. Through the forest! Great idea! Then lightning sets the damn forest on fire, and they run. They tie themselves together and have to jump into that fast river and try to not drown as it sweeps them fifty miles off course. And over the frikkin' falls. It might have been a little easier if Joe knew how to swim.