Well they more or less can be. It's entirely at the discretion of the developer if they want to include the Apple TV version for free with the regular iOS version. Or if they want to charge separately for it.
I'd guess Apple's thinking on it was down to the fact that there can be quite a bit more work involved in making the Apple TV version.
While the code base remains largely the same, there are Apple TV specific optimisations to be done. Reworking controls, graphics, interfaces and so on.
It's not hard work by any means, but it can be time consuming and I believe that's why some developers choose to charge separately for their games on Apple TV.
I don't particularly agree with it myself. Any and all games I release for the Apple TV (if it's a paid game) will always be included with the purchase of the iOS version.
Granted I don't often charge for my apps, I'm just happy if people use/play them. It's not where I make the bulk of my money. It's sort of a hobby for me, just something to keep my mind occupied because I despise doing nothing.
Hmmmm, I do seem to ramble on something rotten when my morphine kicks in
Total tech addict, software developer (more or less) and spouter of complete and utter nonsense when my medication kicks in. (No, really.)