We stayed at Belizean Shores a couple of weeks ago and used Tuf E Nuf for some of the tours and activities that we did while there.
We did the Beach BBQ / Fishing trip with them, and it was okay. I am also a very experienced fisherman (although not for the species we were fishing for and I didn't bring my fly rod with me). The equipment we used for the reef fishing was substandard, the guides were okay....... but not great (I have fished with great guides -- they weren't).
I don't have any thing bad to say about them, and some of the other trips we did with them were quite good.
My opinion (so take this as you wish and I haven't been fly fishing with them), I would probably look for a local who is experienced with fly fishing the flats. I know there are lots of them out there and you can book once you are down in San Pedro - just ask around. Maybe someone will tell you that Tuf E Nuf are great! Just personally they would not be my first choice for the type of fishing you are wanting to do.
To give them a positive note - we really enjoyed the diving and snorkeling tours that we took with Tuf E Nuf.
Hope this helps.