Try this guide to fixing Safe Mode problems:
If the Springboard crash keeps happening, one or more of your installed tweaks is probably incompatible with your device's version of iOS. Open up Cydia, go to Manage -> Packages (or just the "Packages" tab on iPad), and check the descriptions of each of your installed tweaks to try to find out whether they're compatible with your version of iOS. If one isn't, it's probably the reason for your crash, so uninstall it using Cydia. (Also check your packages to make sure they're all from legitimate sources such as BigBoss, Cydia/Telesphoreo, ModMyi, and ZodTTD/MacCiti; pirated packages frequently cause problems.)
If you would like to simply uninstall all of your Mobile Substrate tweaks to start over fresh, search for "Mobile Substrate" in Cydia and uninstall it. This will also uninstall all of your tweaks (since they "depend" on Mobile Substrate), which means you can then start over and reinstall your favorite tweaks one by one, watching carefully after each install to look out for problems. If you're interested in this method, you might first write down a list of your tweaks (or email yourself a list using the free AppInfo tool installable via Cydia) to make sure you remember which ones you should try reinstalling.
Try removing the last installed tweak.