Often you will get a conformational change in the receptor upon agonist/antagonist binding. So, the bound compound changes the electron distribution of the receptor just enough that it's more stable in another state. For AMPA receptors, for example, they're composed of 4 proteins that form, like, columns through a cell membrane. When it's not activated, the 4 proteins are slightly twisted, such that there is no opening between them. With each glutamate that binds, the proteins that make up the AMPA receptor twist slightly, exposing an opening down the middle. The more open the receptor, the more ions can flow through the channel. When an antagonist binds, the quaternary structure of the AMPA receptor is more stable in a deactivated state, even if more glutamate bind. These bindings are typically transitory, so the molecule will kind of "flicker" on and off the receptor, but when concentrations are high, it's more likely to be bound, and when concentrations are low, it's less likely to be bound.

TL;DR: It's about electron charge distributions.