ArisKateris' analogy is:

1. The reasons we want things are atoms.
2. Pleasure is protons.
3. Atoms have more components than protons.
4. Similarly, we want things for more reasons other than the pleasure they give us.
5. Even if every time one of our desires is satisfied, we feel pleasure, doesn't mean that pleasure is the only reason we have those desires. Similarly, even if an atom always has protons, doesn't mean it doesn't also have other components.

You are also making the argument that we want things that don't cause pleasure. Shouldn't this be, in your analogy, an atom without a proton?

ArisKateris should have picked electrons instead of protons, it makes the analogy a little less confusing. Desires without pleasure are like atoms without electrons. These are called "positive ions" and are not totally uncommon.

It personally seems obvious to me that we want things other than pleasure. For instance, I occasionally read books that I hate and am miserable reading because they are part of a series, and I want to complete the series. That's what I want, and I don't care if there's less pleasure in the universe because of my actions.