For my group, it's very common for a quest-giving-entity to offer the group temporary housing. This could be a wealthy patron with a large house, a town mayor who sets them up at an inn, whoever lives in the castle, whatever. In any case, this allows for the players to have a defined safe haven they can return to during longer missions without having to concern themselves with constantly dealing with housing issues.
That only works while the heroes are local, of course. Most missions require some amount of travel. So then you're back to inns, taverns, camping, etc, while on the road. Or finding the safest corner of the dungeon.