Currently there is no way to set-up a short cut key for uploading files to the server.
You can raise an enhancement for the same.
Even if there is currently not an option for setting up a shortcut to do this. The CF Builder is built in Eclipse. There are other FTP tools that are available for Eclipse (not many that are great) that you can utilize. Another option is that you can optionally extend anything in the Eclipse framework using the Eclipse SDK.
If this is something that you really want to add, I would suggest looking over the Eclipse SDK and adding that feature or making a feature request to the CF Builder team. If they do not include it in this release (highly unlikely at this juncture) they might add it in a future release if enough people agree that it should be added.