I'm sure some Democrats were genuinely fearful of the long-term consequences of going nuclear. But it's important to keep in mind that the incentives of an individual senator are often much different than the incentives of his or her party, or his or her institution. Weakening the filibuster would make the Senate a more democratic institution, and give Democrats more power -- and that's precisely why filibuster reform is so problematic for individual senators. Even senators in the majority. If you enjoy using the threat of killing legislation to lock in goodies for your state or paymasters, then you probably don't support any effort that will limit or eliminate your power to impose a supermajority requirement.
The other side of that coin is that a supermajority requirement often allows senators to "support" legislation they're actually happy to see fail. If, say, breaking up big banks is important to your constituents but abhorrent to your party or your donors, then being the 58th vote for a bill to break up big banks is actually hitting the sweet spot.
The same dynamic will hold if and when Republicans take control of the Senate. Which is a decent reason to suspect that they won't nuke the filibuster either; and ultimately why Republicans were eying the budget reconciliation process -- and not filibuster reform -- as their vehicle for passing the Romney agenda had they taken control of government this year.