A lot of people have been asking me about that. So, I wrote some scripts real quick to create a udid-protected repo.
When you add a repo link on cydia, cydia will search for Release and Packages.bz2 or Packages.gzip. So, we just added .htaccess to redirect Release to Release.php and Packages.* to package.php. Inside those php, we check if the requested udid is valid. If it is, just redirect it back to required file.
Check out my github https://github.com/moeseth/UDID-protected-cydia-repo