Once you’ve downloaded the installer, launch Terminal from the Applications » Utilities folder.
To create the install disk, execute this command:
sudo "/Applications/Install OS X El Capitan.app/Contents/Resources/createinstallmedia" --volume /Volumes/Untitled --applicationpath "/Applications/Install OS X El Capitan.app"
Untitled is the name of the destination volume — your USB flash drive.
You’ll have to enter your account password before proceeding. The utility will then prompt you to confirm that the disk can be overwritten. That’s it.