I have a 13" retina. I use the USB ports, HDMI port, and headphone jack regularly.
I never use the thunderbolt ports. I'll probably end up using the SD card slot before the thunderbolt ports.
What do you use them for?
I have several Thunderbolt peripherals at home (Promise Pegasus R6 12TB RAID array, Buffalo HD-PATU3 Thunderbolt 1TB HDD, Seagate GoFlex adaptor for connecting SATA3 drives to my Mac via TB, LaCie Rugged SSD with a 250GB 840 Evo in it, Caldigit TB dock for expansion).
I use them because I do heavy video editing and photography, so I need the speed.
I could have just put the 250GB 840 Evo in a USB 3 enclosure, but TRIM wouldn't work over USB (it works over TB). Besides, I carry it with me all the time.