It's a holdover from the old days when microphone technology wasn't as advanced. The military adopted "dynamic microphones" as the standard, which were less noisy than the alternative "carbon microphones." Carbon microphones required a DC bias voltage to operate, and the dynamic ones did not.
Fast forward to current airplane microphones, which are electret, and still use a bias voltage, so if you plug a military dynamic microphone into a civilian airplane jack, the microphone would burn out from the voltage.
So what? Well, helicopters were originally very military oriented, so they all were wired for dynamic microphones. They used a different jack to avoid accidentally plugging the wrong type of microphone into the wrong type of jack. Even though helicopters are widely used outside of the military now, the standard remains, and many emergency radio equipment (fire, medical, police, etc) still uses the dynamic standard.