OTA updates are usually a good thing, but first impressions can be misleading. The just leaked Android 4.4 KitKat build for the Galaxy S4 seems good, but some behind-the-scenes changes broke SuperSU, making root access difficult. Ever the go-getter, Chainfire already has it sorted out.
The new flashable ZIP file is available from Chainfire's site – version number 1.89. CF-Auto-Root has also been updated to include the new SuperSU. This has been successfully tested with the leaked ROM on the GT-i9505, but should also be fine on other devices you need to get root on.