Coming from the comics:
Generally, the Human Torch has been portrayed as surrounding himself with flame, rather than transmuting his body into some sort of plasma.
If he were truly made of flame, he might let bullets simply pass through him, instead of melting them before they reach him. Similarly, he wouldn't have to worry about dodging large objects thrown at him.
Perhaps the most telling, however, is when he chooses not to engulf his entire body in flame, such as in this scene from Fantastic Four (1961) # 164:
If the rest of his body was simply flame (as opposed to a human body, with bones and muscles), then what's holding his arms where they are, and how is he going to use them to grab that guy and lower him to safety?
That said, I should note that this scene is from a comic published in 1975. It's possible that someone has changed how the character's powers work since then; certainly there have been multiple stories that point out how the FF resemble the ancient four "elements": earth (Thing), air (Invisible Woman), fire (Torch), and water (Mr. Fantastic). this also predates the various Handbooks Marvel has published over the years.
I picked the scene because it was the first one I thought (possibly because it was from one of the first FF comics I bought).
One of the biggest differences between Pyro's power and the Torch's is that the Torch can generate fire, whereas Pyro can only manipulate fire that already exists.
So, to your question: as PlutoThePlanet says in his comment, the Torch doesn't actually become flame. Pyro would be able to use the flame surrounding the Torch's body, and new flame the Torch generated, but not control Johnny's actual body.
And, apparently, controlling the flame surrounding Johnny's body actually allows him to control Johnny's body (similar to how Magneto might be able to control Iron Man's armor, but not control Tony Stark himself), and prevent the Torch from "flaming off."