Well, to take the simplest example of the bond in a hydrogen molecule, you have two positively charged nuclei, and two electrons. Each electron is attracted to both nuclei, but repelled by the other electron. Chemical bonds are then a sort of compromise; it's a local equilibrium where it would take more energy to smoosh them closer closer together or pull them further apart.
That two electrons can be in the vicinity of positively charged nuclei is not without precedent.
After all, Helium atoms have two electrons orbiting each of them and are stable, even though the electrons repel each other.