I think Digsby has recognized user's feelings on this issue and their latest update addresses these feelings directly. The new version makes our grid technology apparent to the user. I think the fact they addressed the issue head-on counts for something.
I also feel that it is important for "free" software to find a revenue stream. While there are several examples of truly free software being sustainable, there should also be a place for alternative revenue streams for companies that want to make software available to users at no direct cost.
Yes, users need to know what's going on. This is uber-important. But assuming they do, alternative revenue streams are a good thing for everyone, IMO.