Usually it’s to create bounce light. Tilting the flash upward turns a small, harsh on-camera light source into a much larger, more diffuse source by reflecting it off the ceiling or other surfaces. That gives softer shadows, more flattering light, and helps avoid the harsh “on-axis” look and red-eye that direct flash can cause.

Even in a large room or church, bounce can still help if the photographer only needs a little fill light and is using higher ISO settings. In that case, the flash doesn’t need to fully light the whole scene by itself.

If the ceiling is truly too high or unsuitable, pointing the flash up may do very little. In that case the photographer may simply be working from habit, or leaving the flash in that position while shooting a sequence under changing conditions.

So the main reason is softer, more natural-looking light; in some venues it works well, and in others it may be of limited benefit.