It’s not about how bad Mubarak was. It’s the fear of what will come. Islamist rule over Eqypt will be worse.
If it is Islamist rule, which is not certain by any means, in some ways it will be worse. In some ways, it will be better.
The unintended consequence about suppressing people in their own country is that it gives them a very legitimate and personal grievance against you.
The Iranians hated us a long time for supporting the Shah. They revolted with whoever was able to do it. Did the ayatollahs turn out to be worse? Sure. Now the current generation of Iranians gets it.
Still, that sort of hindsight is a hard sell to people who are hoping for a better life, while you're financing their hated overlord. We may be stuck with a generation of Egyptians that hates us. We probably earned that. It may take 30 years of Islamic oppression before they get it out of their system.
What's the alternative? Pay billions a year forever to keep them prisoners in their own country? May as well let them do it to themselves, and take ourselves out of the equation.