As far back into my childhood as I remember thinking about such things, I thought of the physical objects around me as made up of particles. I learned last night, in talking to various philosophers, that this attitude in childhood is not universal. In fact, apparently, many educated people have Aristotelian intuitions that material objects are solid and continuous through and through, and while they can think the particle hypothesis, it does not come naturally to them.
This is an interesting case of how theory-laden the "intuitive" can be. To me, it is entirely intuitive to see an object as a bunch of particles, though I wouldn't say that I have a positive intuition that it is so—just a pervasive belief. At the same time, this is a belief I need to think myself out of (and into a suspension of judgment) because I do not think current physics gives one good reason to think there are particles.
This little case study is kind of scary to me. For instance, right now it seems entirely intuitive that space-time be a four-dimensional manifold, with time being ontologically on par with other dimensions. In fact, I've gotten to the point where a philosophical statement that says something like "substance S has accident A at time t" seems clearly incomplete: I want to know which reference frame this is in, and how the accident is spread out in a space-like hypersurface.
But since these intuitions are highly dependent on a physics that might turn out to be wrong (quantum theory and relativity theory are not both true, since they are incompatible), I need to be more open to three-dimensionalist ideas, which I find kind of scary. Three-dimensionalist ideas induce a kind of conceptual vertigo in me—the thought that I am this three-dimensional object in some kind of flow of time is weird, though I do of course think such metaphors sometimes.