Air pressure. Google "ISP". Rockets are more efficient at lower air pressures, preferably vacuum. But a rocket (really just the bell/nozzle bit where the fire comes out) must still be designed to operate in a particular air pressure. The problem with the first stage of every rocket is that is must travel between sea level a near-vacuum at high altitude. So you cannot ever reach proper efficiencies. By launching at altitude they can optimize for vacuum operation without worry about sea level performance. We are talking about roughly 10~% margins here, but rocket companies can spend billions on 1-2% improvements.

Also, by launching from an aircraft over an ocean one can avoid many of the ground realities of rocket operations. Land-based sites much deal with shipping notices and noise issues. Stratospheric can fire these things in different directions, to different orbits, without worry. They might also be able to launch multiple rockets on a single flight, a totally new service that might hit an unexplored market.

Lastly, politics. Stratolaunch could travel the world to launch rockets from basically any big airport. So if the Saudis want to launch something without the hassle of US/Russian security checks, they can have Stratospheric show up to handle the launch locally. There are probably enough countries wanting to launch something locally for prestige alone.

Or... someone just wants to have the biggest airplane in the world (paging Dr. Freud) and this is the way to make that happen.