It's punishment and there to deter other clubs from going Bury's way....I think.
They did it to my home club Luton a long time ago - a double whammy in fact. This from Wiki:
"The 2008–09 season was the 123rd season in the history of Luton Town Football Club. The team's 24th-place finish in League One in 2007–08 meant the club competed in League Two. The club was docked 30 points at the start of the season; 10 by The Football Association for irregular matters involving player transfers, and 20 by the Football League for breaking rules on exiting administration. As a result, the club finished bottom of the league and was relegated to the Conference Premier. The season was not, however, without success – Luton beat Scunthorpe United 3–2 at Wembley to win the Football League Trophy for the first time."
They might as well just have thrown them out of the league instead of docking the points because they stood no chance of surviving with a 30 point deficit and the loss of some players after the relegation. It took quite a few seasons for them to get back in as well. They're going ok now though, after a couple of promotions, and are back in the Championship this season.
Although not as severe, its a crippling blow for Bury and rough on the fans (who did nothing wrong). I feel sorry for them.