Time passes quickly. It's much later than I expected. <<<<

time goes by quickly

It means time goes by very quickly. We often hear this sentence: "Time flies when you are having fun."

Time passes very quickly

The term "flies" or "flying" can mean moving quickly, in addition to meaning moving through the air. You could say "That car is flying around the track!" and you would not mean that it is in the air, but going very fast.