I also don't like the comma; I guess the colon would be OK, although it does look a bit ... extreme, maybe?
Maybe the confusion comes from sentences like this:
The thing is, he's really fast.
A comma is OK here, as "the thing is" is more of an interjection or introductory clause, or whatever it's called, similar to "in fact" or "actually". It isn't the subject of the sentence, which becomes apparent when you say "The thing is ..." and someone else snaps "Yes, what is the thing?!"
" the thing is (informal) used to introduce an important fact, reason or explanation: I’m sorry my assignment isn’t finished. The thing is, I’ve had a lot of other work this week. "
http://www.oup.com/oald-bin/web_getald7index1a.pl"The fact of the matter is" sounds a bit similar, but in fact I think it isn't, it's the subject, as Jgmci says.