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You can remove Cydia from your device without losing your jailbreak. Without Cydia, your device won't be able to boot into safe mode if something goes wrong with your jailbreak. This will open a list of all of your installed packages. This will open its Details page. This will add the item to your uninstallation queue. This will allow you to select more packages to add to the uninstallation queue. Return to the "Installed" tab after you have finished queuing. This will remove all of the packages that you have selected. This will display a list of just the most important packages. Open the "Cydia Installer"" Details page and tap "Modify". Select "Remove" and then tap "Confirm". Cydia will be uninstalled, and your device will reboot afterwards.
Open Cydia. Tap the "Installed" tab at the bottom of the screen. Tap a tweak or app that you want to remove from your device. Tap the "Modify" button in the upper-right corner and then tap "Remove". Tap "Continue Queuing". Repeat the queuing process until you've selected all the packages you want to remove. Tap the "Queue" button and then tap "Confirm". Return to the "Installed" tab and select the "User" list. Uninstall the "Cydia Installer" package.