Note that not all tweaks incompatible with iOS 6 will cause this "shrinking Cydia" effect; it is just one kind of tweak incompatibility. (WinterBoard is compatible with iOS 6.)

The issue that may show up after rebooting may look like this (yes, that's a tiny Cydia):

Or it may look like this:

If you run into this problem, you can fix it via rebooting your device while holding the volume up button, which will boot it up with all tweaks disabled. This will let you uninstall the incompatible tweaks from Cydia. Then reboot again to enable tweaks.