I can copy El Capitan installation on thumb drive but it is not visible when I hold option key on restart
(Download the latest El Capitan Installer (10.11.3))
Open Terminal and check the hash of InstallESD.dmg:

shasum /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/SharedSupport/InstallESD.dmg


The result (as of March, 5th 2016) should be: 526a6f7a619ef86f42acc026276aab351ea27614
Insert your thumb drive
Get the disk identifier of the thumb drive with

diskutil list


Below I assume the disk identifier of the thumb drive is disk1
Delete any MBR on the thumb drive:

diskutil umountDisk /dev/disk1
sudo dd if=/dev/zero of=/dev/disk1 bs=512 count=1
diskutil mountDisk /dev/disk1

Open Disk Utility and partition the thumb drive:

Options...: GUID partition table
Name: Untitled
Format: Mac OS X Extended (Journaled)
Create the El Capitan Installer thumb drive:

sudo /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Resources/createinstallmedia --volume /Volumes/Untitled --applicationpath /Applications/Install\ OS\ X\ El\ Capitan.app --nointeraction


The output looks like this:

Erasing Disk: 0%... 10%... 20%... 30%...100%...
Copying installer files to disk...
Copy complete.
Making disk bootable...
Copying boot files...
Copy complete.
Done.

Check the InstallESD.dmg on the thumb drive:

hdiutil verify /Volumes/Install\ OS\ X\ El\ Capitan/Install\ OS\ X\ El\ Capitan.app/Contents/SharedSupport/InstallESD.dmg


The output should look like this:

Checksumming Protective Master Boot Record (MBR : 0)…
Protective Master Boot Record (MBR :: verified   CRC32 $8A0AD7CD
Checksumming GPT Header (Primary GPT Header : 1)…
 GPT Header (Primary GPT Header : 1): verified   CRC32 $E61CC7FE
Checksumming GPT Partition Data (Primary GPT Table : 2)…
GPT Partition Data (Primary GPT Tabl: verified   CRC32 $8F9F9AF5
Checksumming  (Apple_Free : 3)…
                    (Apple_Free : 3): verified   CRC32 $00000000
Checksumming EFI System Partition (C12A7328-F81F-11D2-BA4B-00A0C93EC93B : 4)…
....
EFI System Partition (C12A7328-F81F-: verified   CRC32 $B54B659C
Checksumming disk image (Apple_HFS : 5)…
.................................................................................................................................
          disk image (Apple_HFS : 5): verified   CRC32 $F1A0F123
Checksumming  (Apple_Free : 6)…
...................................................................................................................................
                    (Apple_Free : 6): verified   CRC32 $00000000
Checksumming GPT Partition Data (Backup GPT Table : 7)…
...................................................................................................................................
GPT Partition Data (Backup GPT Table: verified   CRC32 $8F9F9AF5
Checksumming GPT Header (Backup GPT Header : 8)…
....................................................................................................................................
  GPT Header (Backup GPT Header : 8): verified   CRC32 $5826D5C7
....................................................................................................................................
verified   CRC32 $BE5D6293
hdiutil: verify: checksum of "/Volumes/Install OS X El Capitan/Install OS X El Capitan.app/Contents/SharedSupport/InstallESD.dmg" is VALID


Some of the CRC32 values may be different in your output!
Reboot you Mac with the thumb drive attached and hold the alt/opt button. If the thumb drive doesn't show up on the first run just repeat the step. It took me 2 tries to successfully boot to the installer thumb drive.