From what I googled up, it doesn't seem like anything I would call humanitarian.
It seems that while the group had originally been formed to help rafters, by the founders' own admission (under oath, in court), by the time of the flight their mission had turned political, and among other things they were violating Cuban airspace (again his own admission) to drop political leaflets on Havana (again own admission). This despite a warning from the FAA (per testimony of the FAA official who gave the warning, in court) to stop violating Cuban airspace already because it might get them shot down.
Said founder being (again his own admission, under oath, in court) a former CIA operative. Involved in the bay of Pigs invasion. Also one who directly shelled a Cuban hotel with a 20mm cannon at a separate point in the sixties. Also also someone who (on his own time - at least by his claim) f000lew supplies for the contras in the eighties.
You know, I can think of plenty of reasons for Castro to want those planes shot down that DON'T involve wanting to sabotage the peace process. Something like "Let's see, a known agent of a foreign power who is assisting anti-communist groups the world over and has participated in both an invasion and acts of terrorism on Cuban soil has flown a plane to drop leaflets over my country that tell my people my government is a bad government...what do I do about this?"
None of which make the shooting right (especially as they didn't wait for the planes to violate cuban airspace to shoot THAT time). But it doesn't theories about wanting to derail a normalization process.