One of link's weaknesses is his obvious weakness to pressure. Take him to stages like Warioware and such. In a way, he's very similar to Snake in that you have to really get in on his space and never leave. You want to be an insurance salesman. Once you get past the beartraps and dogs, get your foot in the door, talk your way in and try and give Link bad insurance that won't, in fact, cover any of the damage he could realistically attain.
On a slightly less confusing and silly note, if you can keep him from zoning [platforms and large stages help Link here], you can generally kick his teeth in. Yes, his nair is dangerous, but it has a decent amount of endlag, as does his up-b. If you can either bait or dodge his nair, the punish must be swift and unyielding.
If you really want to do a Ganon vs. Link matchup, learn to powershield. That's essential. His boomerang is probably the best projectile to try and counter. Also, don't always expect to get the hardcore dunk/stomp punish. Don't be afraid to use your nair as a quick-punish tool of pain. Once you get through Link's projectiles, remember that many of his aerials and close range tools have lengthy endlag [excusing the dair, which is very quick and the nair, which has a lingering hitbox]. Assuming you can effectively bait things like the uair, you can fairly easily smack him with a dunk. Just remember to be patient with your punish timing, and while you should keep up the pressure constantly, do not get overzealous or greedy, as that's a sure-fire way to get yourself hurt. Last thing, Link's nair, while quick, does not make him invulnerable. The range isn't stellar nor is it disjointed, so if you can bait it, you can get in a good punish dunk. Also remember that the vertical range is exceptionally poor, so be sure to abuse Ganon's uair, or, in the unlikely circumstances, mash his face in with a stomp. This makes a lot of assumptions about you getting past his projectiles [which is no easy task], but once you get in on link, he is beatable.