It's insane to think they'd purposely mess up their products so you'll buy dongles. They have an overall strategy they are executing. You might thing it's wrong, but it's just like the decision to remove the headphone jack.It is still more money, it doesn't matter how much, it is simply more money than they use to make. There is a huge profit margin on dongles, great ROI.
It's like saying Apple should ship every iPhone with a small scratch in the screen and then sell a buffing compound to remove it. They would never do that.
The thunderbolt ports are versatile and have many advantages. There are tons of reasons they'd want to do this, but it's not to make money on dongles...don't be so daft.