MobileSubstrate did not cause the problem, no, one of the apps that relies on MobileSubstrate did. Do the following:
1) Go to Cydia>Manage>Packages>Mobile Substrate>Modify>Remove.
2) Note all of the packages which will be removed so that you can reinstall them at a later date.
3) Click confirm to uninstall.
This will uninstall Mobile Substrate and all packages that depend on it.
When done, restart your phone (hold power for 5 seconds, slide to power off, wait 10 seconds, restart). This should have fixed your problem.
You can then re-install any of the packages you noted in step 2 that you still want, one at a time. You should probably restart between each package you install. If at any point you get the Safe Mode message, the last package you installed is probably the culprit.