It's only bonus content because they decide it is so they can nickel and dime people. It shouldn't be. It should be available to everyone that bought the game.
First of all, this amiibo content in Super Mario Maker can be unlocked regulary. That was confirmed various times.
Second, I personally don't see this at all.
I just bought Yoshi's Woolly world. And 2 Yoshi amiibos.
Why do you ask?
Because I wanted to get the extra skins? Nope. Because I actually wanted the amiibos. Because they are really cute. They unlock extra skins inside the game, which are basically pointless? Now that's nice. Would I buy those skins? Nope. Would I buy an Amiibo to get those skins unlocked? Nope. It's simply a bonus, that I'm getting for buying the Amiibo.
Nickel + diming would be to sell those skins for let's say 0.50EUR each in the eShop. Or would you be happy, that you could unlock the skins without buying Amiibos?
Maybe it's weird to see it that way, but that's how I see it.
Let's just look at the current amiibo support:
Mario Kart 8: racer suits
Smash Bros: train your amiibo
Hyrule Warriors: get items every day and 1 extra weapon for Link
Splatoon: play single player maps again beating special challenges to get exclusive in-game gear
Captain Toad: hide and seek 8-bit toad search challenges
Rainbow Curse: basically make the game easier once per day
Codename Steam: 4 amiibos supported for extra team members
Xenoblade 3DS: get points/stars to unlock bonus content (which can be gotten via streetpass or coins too)
Woolly World: get special Yoshi skins for each Amiibo and the plush Yoshis unlock a second copy in the game
(i hope i haven't forgotten a game)
Is that a problem? I would say no. Especially when the current industry-standard is to sell single missions here and there for a few bucks each. Without giving me something physical, that I actually want.
You could probably complain about the single Hyrule Warriors weapon. I personally don't have an actual problem with that, simply because Hyrule Warriors has insane amount of content already and I'm using the master sword anyway.
If you actually buy an amiibo just to get one of those minor features, then I don't know what to say. I sure wouldn't. I would probably buy Shulk at some point. Why? Because I want to get extra points/stars? Nope. Because I actually want Shulk. I got like 700 points/stars via streetpass anyway.
Or let's look at those timed Virtual Console demos. Would you buy an Amiibo to unlock that? I sure wouldn't. But it's nice that I get 3 minutes of playtime just because I own one of those.
Or do you also complain about for example games, where you can unlock extra stuff in case you already own the predecessor? There are quite a few of those. And you could see it for those the same way. "What? I'm supposed to buy the predecessor although the content is on disc? Rip-off!!!". I see it - at least for the games that I own and that have that feature - exactly the same as the amiibo support. I'm simply getting something minor on top.
Predecessor/other game unlockables:
Professor Layton: entering the key of another Layton game gets you additional content
Tales of Xillia 2: unlock certain costumes in case you got a saved game of Xillia 1 + Graces
Darksiders 2: bonus items when you played the predecessor
Metroid Prime 1: NES Metroid + Fusion suit when you connect Metroid Fusion via GBA cable
Zero Mission: unlock all pictures including additional concept art when linking with Prime or Fusion, not sure