X-Plane ATC is not as smart or flexible as a real, human ATC controller is. In many cases, this means that it doesn't direct airport traffic in an efficient or quick manner. If you have any AI aircraft enabled, you may be encountering this--an AI aircraft may be blocking the runway, attempting a landing, etc. and ATC won't let you progress. Or weather changes affecting an airport flow could also be an issue if you don't use AI aircraft.