In addition to the good answers of others: sometimes, pitchers even intentionally throw four balls, throwing the ball meters wide, sometimes behind the batsman's back (the catcher will know such a throw is coming, and move to catch the ball)

That can happen, for instance, if second base is occupied and two men are out. Giving a batsman a free run changes that into a situation with still two men out, but first and second base occupied. With first and second base occupied, if the next batsman hits the ball, all three players have to run; that make it easier to get the third out needed to end the (half-)innings.

It also can be done if the man at bat is a particularly good hitter, and the next ones at strike are deemed less of a danger. For example, with third base occupied, it's highly likely that a good hitter will hit the ball in such a way that the man at third base can score a point; that risk is lower when facing a not-so-good hitter. Therefore, the pitching team would prefer giving away that free run and have the lesser player take a go.