Something that is proportional (1) forms a whole with other quantities, or (2) is considered quantitatively with respect to something else. Proportionate means in due proportion. The distinction is subtle, but proportionate describes something that is made that way by an active agent, and it often describes quantities that are difficult to measure. Proportional doesn’t necessarily involve an active agent, and it is the preferred term where actual measurements are concerned.
Still, because the difference between proportionate and proportional is so subtle, writers who don’t grasp it need not worry too much, because the words are indeed widely used interchangeably. When in doubt, use proportional, which is twice as common and broader in meaning.