I don't follow this logic. Amazon did something bad on their app store so now walled gardens are good?

No, the logic is that several large companies (Amazon, Apple, Microsoft) have done bad things on their app store, so no stores can be trusted. But for me, I trust a big name store more than I trust an small unknown store.

Walled gardens are good because if you insist on picking your fruits only from the wilderness due to moral principles you're gonna get mauled by a bear some time. Sure, you might prioritize feeling morally superior, but the majority of society is more practical