Ganondorf has approach issues.
He has no projectile. You can't win by playing defensively against someone with a projectile when you have none. They will shoot you until you die. You have to go on the attack if you want to win. This is a problem for Ganondorf because he's a big target, has slow movement speed and has truckloads of cooldown lag for just about all his moves. Usually by the time he's gotten close to his opponent Ganon has been hit half a dozen times from lasers or arrows or whatever. Typically, the opponent either flees to a safer vantage point while Ganon reels from the last hit OR they zoom up to him and continue to lay down the hurt with juggles, which Ganon is terrible at escaping being heavy, or grab combos, which Ganon is also terrible at escaping for exactly the same reasons.
"But wait, how does everyone else with no projectile deal with this junk?"
-Typically with speed and mobility to weave between attacks and strike before the shooter can react. Think chars like Jigglypuff, Kirby (though he shoots sword energy, it's a rare moment when that overcomes projectile spam), Meta Knight, Squirtle, Sonic and Wario. These guys can either go under, over or between projectiles while making headway to their target and since they're not being hit, they can attack freely or move accordingly with their opponent. Most of them are by no coincidence, short.
"What about the guys you didn't list like Bowser, or Donkey Kong or..."
-Yeah shut up, I was getting there. Guys like Bowser, Donkey Kong, Ike, Charizard are pretty much in the same boat as Ganondorf when it comes to dealing with projectiles. Being big and slow, they suck at it.
"Then what makes them any better than Gan..."
-Well they each have quirks that gives them an edge where Ganon can not compete. I'll make a small list:
Bowser has the range and power of Ganondorf except Bowser excels with a great grab game, a very excellent up-b move that helps him break out of locks and combos, and moves with less lag (I'm thinking jab and fair). Also he breathes fire, which gives him excellent range and priority.
Donkey Kong has even more range than Ganondorf with just as much power. He also is much faster in just about every aspect. Furthermore he has deadly grab game. And super armor on key moves (up-b and monkey punch). And he has great edge game and is a menace with his b-airs.
Ike has Ganon's range and power. The fact that he uses a sword gives him priority over anyone else's body parts. Furthermore, he has an annoyingly good jab that can combo into itself or other deadlier moves (keep in mind his jab can also kill -_-), a move that can counter other moves, making him invincible and nullifying the attack no matter how powerful while dealing excellent damage to the offending attacker, and his up-b is extremely hard to spike, gimp, guard against.
Charizard has range and power. His rocks and fire give him a ******** amount of priority, damage and knockback (his f-air is fire). He also has faster ground speed. And he has multiple jumps and can glide.
Addendum: Marth uses a sword which makes him better than Ganon. The fact that he's also fast, has good range and maneuverability, chain grabs, side-b combos and a counter move put him well above many other people as well.
Captain Falcon is an unfortunate case. He's fast, but has crap for priority. And his kill moves are either tough to land or are otherwise easily avoidable. Other chars just flat out beat him with priority or otherwise outlast him. Even Ganon has a chance against him because of this.
I could probably write pages more on Ganon's faults and advantages other characters have over him, but that's what the match-up threads are for. Check them out, they're stickied.
tl;dr People hit Ganon, and he doesn't hit them. That's why they win and he loses.