Yep. It's pretty much a long-shot to catch a 6IV Ditto. If you need it for IV breeding though, my advice to you would be to just fill up one of your PC boxes with 3, 4, and 5IV Dittos from the Safari and use those for your IV breeding.
It really doesn't take that much longer to breed a perfect Pokemon using just 3IV Dittos than if you had a 6IV in my opinion. Just match up the missing IVs of your Pokemon with one of your Dittos. One of those Dittos in the box will have the IVs you need. (It's a good idea to "mark" them according to what IVs they have to keep track of them all while you're collecting them too). =)
And hey, you might get lucky and catch a 6IV while your collecting your Dittos for your full box, or even a shiny from the apparently increased chance of catching one in the Friend Safari. (I didn't though) It's still defiantly worth it in my opinion though if you plan on IV breeding.