In algebraic set theory a la Joyal and Moerdijk, the subset relation *is* taken as fundamental, with membership only being a derived notion (specifically, the cumulative hierarchy is taken to be the free "ZF-algebra"*; i.e., partial order with small joins and an abstract "singleton" operator. The order corresponds to subsethood, and x is defined to be an element of y just in case the singleton operator applied to x yields a subset of y). I can never quite grasp what it is that mereology is supposed to be all about as a supposed contrast to set theory, but if it's just a matter of viewing subsethood as more elementary a concept than membership, well, there you go.

[*: ZF-algebra isn't a great name for the general concept of such structures, in my opinion, since they have very little to do with specifically Zermelo-Fraenkel set theory. Note that, while every object in the cumulative hierarchy is uniquely a join of singletons (and in this way can be viewed as a plain old bag of elements), in more general ZF-algebras, there may be objects which are not joins of singletons, thus carrying a more mereological flavor; in particular, these illustrate that subsethood is not definable in terms of membership, firmly establishing subsethood as the more primitive notion in this context]