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.
Chainfire is still undecided about adding this version to the Play Store as it is only for a single leaked ROM. Updating through Google Play will cause a binary update, which is a hassle for everyone. The Play Store rollout might have to wait for the official OTA to start hitting devices.