There is never a safe upgrade. Even if millions of beta testers ran the installation script and nothing bad happened, they didn't have your system and your data. If your filesystem has errors, you can render your Mac unstartable by running any system update. Running a migration script could delete files you care about, could break your software, or could expose damage that already exists.
For those reasons you should always back up your Mac and estimate how long it would take you to wipe the Mac, re-download the installer (if you don't save a copy) and then re-run the migration. If you don't have time to do a complete restore or the copies of OS and procedure to recover, you should probably pass on the update.
If you have a backup plan that makes a bootable backup of your OS, you could simply test one of those bootable backups before letting the installation run on your Main OS - keeping the backup handy and safe.
If you don't have a bootable backup, then you might spend more time and install a clean El Capitan onto a USB hard drive and then migrate the data from your current boot drive.
Then you can use the Startup Disk system preference to choose to boot into 10.11 or 10.10 for as long as it takes to make sure your critical apps and settings are compatible with 10.11. Either way, you'll need to look over all your Apps - potentially apply updates to them or wait for vendor engineering and QA to release changes needed for 10.11.
- homebrew already has changes for 10.11 but it's explicitly not supported, so there will be time and breakage anticipated on that front
- zsh shouldn't be a large issue, but again - until you test your setup - who can guess...
That removes the pressure and stress of having all your eggs in one basket. I've been running 10.11 for quite some time and it's actually more stable for what I do than 10.10, but that's probably not everyone's experience.
You could always be lucky, install the 10.11.0 build with no backups and no contingency plans, but I wouldn't advise it without some prudent preparations in case your upgrade doesn't go smoothly.