As others have said, there is a short-ranged and attractive “strong force” that is much more powerful than the repulsive force of electromagnetism that you are referencing when talking about the protons repelling. An interesting corollary: what if you had an atomic nucleus that was so large that it was almost the range of the strong force, and you stretched it along one axis? At the right amount of “stretching,” the nucleus would behave like two separate nuclei right next to each other, and repel with great violence. This is what happens with nuclear fission, and is why you don’t have to “smash” heavy atoms apart, you can just sort of jiggle them with a neutron.
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