Samus is really frustrating and boring to play against. Between her camping and edgeguarding, you're going to have a hell of a time trying to get to her.
Learn to powershield, it's the one thing you're counting on in this match-up. Knowing when to powershield whether it's her zair or the missiles is the goal. If she's at the peak of here short hop and starts pointing her arm gun at you, expect a missile. If she's not doing anything or it's an airdodge from a short hop, she'll most likely zair right before she lands. Learn the powershield timing of both. Since Ganon's so tall, Samus might try to buffer a zair right from the start of a short hop, it comes out pretty quickly so you can't powershield on reaction. If you do predict that form of zair and powershield it, rush in and try punish quickly because she'll still have some lag until she lands.
Distance is another thing that Samus likes to exploit. From far away she will just camp you to death, mid range she will try to follow up from her camping moves (ie. Missile > dash grab), and close range is her trying to hit you away for some more camping. Missiles and zair autocancel the instant they touch the ground. If you powershield a missile from mid range, try to roll away, spot dodge or fullhop/airdodge to dodge her follow up. If it's a dash grab then you have a lot of punishing options. Zair follow ups are usually dash attacks or dash grabs. If you're mid range and she's going to zair you, roll away. To punish her buffered attack.
After a while you have to mix things up. Even though it's Samus, she's not going to do the same thing everytime and get punished for it.
Offstage is really gay for Ganon. I'll say it right now, never try to risk a fair, you'll just get edgegayed. The only thing you should be doing offstage against her tipmaning, and ledgedrop uair/bair. Even if you miss these you can still land on the stage and not get edgehogged by her zair.
If we're recovering, we don't have much hope of recovering unless the Samus only uses Zair edgehogging once or we can land of the stage. We can wait a little bit if she zair edgehogs to hit with the tip of out UpB. It's not guaranteed to work but the more you know.
30 : 70 This is the best Match up I can give Ganon, we have answers to her camping but they're all pretty circumstancial. You have to play absolutely perfect to beat the best Samus'.