Because they only needed a majority to pass the rule change. There wasn't enough opposition to cause a filibuster, which was the point. There was enough opposition to do a filibuster when 60 votes were needed, now that only a majority is needed a filibuster is pointless. Thus, the minority might as well go home if they face a united front from the majority on the specific points this rule change covers.
I may be wrong, but I believe Senate rules are set by majority vote, and there is a mechanism available to the Majority leader to simply declare only 50 votes are needed to pass. The main reason it isn't used all the time is that the majority party generally worries about repercussions when they are a minority party.
If it is limited to Senate rules changes then it's irrelevant. The Senate rules are, after all, the rules. For example:
Majority wishes to pass a bill that the minority doesn't agree with. Majority wants to change the rules on that vote to get it passed despite minority.
Minority says they can't because the Senate rules forbid it.
Majority changes rules from forbidding it to allowing it.
Granted, that's a simplistic way of looking at it. It would seem to me that rule changes should have higher requirements than simple majority because then the majority can change the rules whenever they wish.
The power of precedent and fear of being in the minority is what generally fights against this. Rule changes that drastically favor the majority will hurt them when they end up in the minority.
One of the very few enumerated power in the Constitution is that the Senate and House get to make their rules however they see fit. What usually happens is that at the beginning of the new Congress the first order of business for each body is to set the current rules. Part of those rules are how to change the rules during the current.
