Yes and no.
Rarely do you see a giant brainy dude. For example Strong Man, Colossus, and Juggernaught are all super huge guys with superstrength/invulnerability powers. None of them have genius level intellects though. The only big genius I can think of is Professor Hulk (Hulk's body, Banner's mind) from the '80s, but that didn't last.
Most geniuses on the hero's side have fairly normal human proportions, though usually well built and ripped. Mr Fantastic, Tony Stark, Ted Knight, Batman, Mr. Terrific, Ted Kord, 1/2 of Firestorm. However Bruce Banner and Peter Parker have been getting shafted over he last 10 years or so. Banner went from a normal 5'10"/180lbs to a 95lb weakling. Ever since Tobey McGuire was cast as Spider-Man, the comics seem to show Peter Parker as a smaller, weaker, nerdier guy.
The evil geniuses tend to be more deformed or smaller physically. Dr Sivana or the Leader are prime examples, while others like MODOK and Hector Hammond are the super deformed types.