Deleted scenes are scenes written, filmed, sometimes even finished before being chopped off the film for a variety of reasons.
If the pacing of a film is too slow or the pacing of a scene is too slow, bits of some scenes and sometimes whole scenes can be cut. Example: The original "Philo's World of Science" gag in UHF
Sometimes a certain scene tries to make a point that has already been made earlier in the film. Therefore, the scene is cut. Example: "Nemo in the sewer" in Finding Nemo
If a film is too long, some expendable scenes are deleted to shorten the run.
A scene that comes out the way the director or studio doesn't want it to come out is sometimes reserved for the chopping block.
If a scene is too violent, it will sometimes be cut for the sake of ratings or the viewer's stomach. Example: A LOT of the cuts in The Black Cauldron