Ganondorf main here!
I've had trouble in this matchup and I'd give a slight advantage to Charizard. For other matchups, Ganondorf can edgeguard with dair, up-air, or bair, or tippered up-air so that the opponent cannot recover high enough; but not against Charizard because of the third jump and super armor on Fly. Charizard is also heavier than even Ganondorf himself and can mix up his recovery with Flare Blitz, so Ganon has a pretty hard time stopping Charizard offstage. Charizard then has an easier time edgeguarding Dorf with Flamethrower, with Dorf taking lots of damage just trying to recover.
Charizard wins the neutral because Ganondorf's risky approach options have a hard time getting past Flamethrower/Zard's range, and Zard's Fsmash can sway back to avoid an approaching dash attack, Wizard's Foot, or Flame choke, or just power through with invincibility frames. Zard's grab range and run speed help control neutral as well. It's also harder for Ganondorf to punish a landing because of the multiple jumps and Rock Smash, but...
If Ganon can get in, he can combo Zard's big body and weight for lots of damage at lower percents. Dorf's aerial's frame data and decent range are good for controlling aerial space and punishing a Zard getting too close. A misused Flamethower can be punished with Dair and more. Ganon will hit hard; a bad read by Zard or a predictable landing can mean an early kill by smash attack.
That's all I can think of for now. I think Charizard advantage around 55-45, possibly more