Who is complaining about the Flappy Bird clones? If the creator hadn't pulled the app, he still would have been printing out money for the foreseeable future, so I doubt he's enraged about people profiting from the idea. Out of those thousands of clones, the new winner won't be the app that carbon copies Flappy Bird most effectively, it's going to be an app that builds on the idea. If King.com, with their newfound millions, can't build a superior product to some poser "Sweets Smash Story", then they don't deserve to stay on top of the App Charts.
As far as I have seen, the only people who have complained about flappy clones have actually just complained that flappy clones are 'trending', not that clones are made. In other words, they are just annoyed by being bombarded by clone after clone.