I had this same issue when i put in a bad path for a repo. The solution is to use iFile and go to /etc/apt/sources.list.d and edit the file cydia.list and remove the bad repository. You can just backspace it out and leave the file blank. It worked for me perfectly.
Damn. Wish I knew that. Well now im have a whole another problem. When I open cydia, their are NO packages. How can I re-install without losing everything? I cant even search for anything cause nothing shows up