Very good point RE people. Running AWS is expensive, I'm sure, but to be clear, I'm not advocating for bandwidth to be free. Just that $0.08 per GB is not competitive.
Also, since CloudFormation is a feature that facilitates creating more resources that you do pay for I'm not sure that is a great example. That is more like saying that the other services subsidize the Web Console. CloudFormation is not a product in-and-of itself, it is more a shared feature that spans product lines.
Code Pipeline is an interesting one in that if it is true it's not widely used and costs more money than it makes, that's a no brainer: shut it down. But there has got to be more to that story why they haven't.
But in any case, with code pipeline there is a clear value chain that ends at ECR/EC2/Lambda/etc. My guess -- and it is just a guess -- would be that someone feels pipeline produces more revenue for EC2 (or similar) and that covers the cost. Or, simply, they have a path for it to be profitable.