Simple: those small particles still have mass and therefore should still have gravity. Neutron stars are a great example. As I understand them, the star's own weight causes protons and electrons to fuse into neutrons and the collective gravity of the neutrons then holds the star together, even though individual protons are very small objects and individual electrons are even tinier.

Keep in mind also that stars are mostly hydrogen - which essentially has the same mass as a proton. And yet, a star's gravity is strong enough to keep the hydrogen in. Nebulae are hydrogen gas (two protons) and gravity holds them together. Electromagnetism doesn't apply since both forms of hydrogen are electrically neutral and lack magnetic fields. The strong and weak nuclear forces don't extend beyond the individual nuclei, so they're irrelevant. If gravity can affect masses as small as a proton, why should it have a lower limit? What about the idea that so called 'WIMPs' - weakly interacting massive particles - account for the missing dark matter in the universe? Some of the particles in question aren't much bigger than a proton but taken as a whole have profound gravitational effects. Why should gravity stop just because you've taken something apart? Put another way, general relativity says that it should be possible for two neutrons to orbit a common center of mass in well-defined, completely predictable orbits. Quantum mechanics says that would violate uncertainty. Something has to give.

And that's one of the fundamental differences between general relativity and quantum mechanics. You're right that in some situations gravity is going to be overpowered by other forces, but that's not always the case. Either way, the gravity is still there. The cores of black holes may be point-like objects. However, if you have an electrically charged black hole, gravity is overpowering the electrostatic repulsion that should be causing the black hole to fly apart. Since that's happening on a small scale, quantum mechanical interactions *must* be involved. We're 99.9% positive that black holes exist, and yet there is no quantum mechanical theory of gravity that's been experimentally proven and no indication as to where the boundary between very large (GR) and very small (quantum) lies. Or, put another way, why should GR stop working when you get to the singularity when it works beautifully everywhere else in and around the black hole? Gravity *must* work on a quantum level, but there is no understanding of how it's affected by the uncertainty principle and the wave/particle duality of matter and energy.

The other big problem is that both theories offer distant explanations as to what gravity is. General relativity says that it's the curvature in spacetime. Quantum mechanics predicts that it's a force carried by gravitons. *Both* predict gravitational waves, although those have never been detected. This isn't as simple as saying that one theory is right and the other is wrong because gravity still *acts* like the other forces. If it's curvature, it still produces an effect analogous to unlike charges attracting each other. If it's a force, why does it work so differently than other fundamental forces (i.e., why is there no gravitational repulsion?)? Scientists keep looking for some way to explain these similarities and differences and neither theory seems to be able to bridge the gap.

Hope that helps.