Manuals are faster mainly because the engine has a direct mechanical connection with the transmission, whereas an automatic uses a torque converter which is a fluid connection (there's actually no mechanical connection in any gear except overdrive in your standard production automatic....transmission fluid flow is running the show in there). The result is loss of energy transferred.
Now a racing transmission is a completely different beast, and no human can possibly outshift a built racing auto transmission. The real deal with manual VS auto is the fact that if you mash the gas in an auto, the car does the work. In a manual, there's many ways to screw it all up, from miss-shifts, to short-shifting, to tapping the rev-limiter, etc....so a team that builds a car to race because that's their INCOME will typically never use a manual...there's too many variables to be consistent.
I have a tendency to go too deep, I hope I didn't totally blow past your question there.
Cliffnotes: Yes, if you compare production-release versions of a manual or an auto transmission, the manual will be faster. But there are ways to make an auto tranny perform better than a manual. And most high-end race teams use automatics, but those transmissions can't be used on a street-driven car.