This has been driving me crazy for years. There is no reason you should only be able to minimize this application when there is an active connection. The application UI doesn't need to work this way and this is arguably bad UI design. Compare with the way Filezilla works.
Here's a use case: I'm connected to a SFTP site at work. At the end of the day, I sleep my laptop and take it home. At home I connect to a different wireless network, and use the laptop there, but will not get back to what I was using SFTP for until tomorrow at work again. I've lost the SFTP connection of course, but I can't minimize the damn window. I can just close the whole thing, but I shouldn't have to, and I'd like to begin exactly where I left off, with the same folders in the local and remote panes, the history of commands, the history of paths in the drop down boxes, etc.