I'm getting kind of sick of this "deep learning is a black box" trope, because it's really not true anymore. Yes, it's a black box if you just use "some data and 20 lines of code using a basic deep learning API" as mentioned in the article. But if you spend some time understanding the architecture of networks and read the latest literature, it's pretty clear how they function, how they encode data, and how and why they learn what they do.
Because neural networks are so dramatically more effective than they used to be, in so many domains, it's true that we don't yet have a good understanding of optimal ways to build, train, and optimize networks. But that is exactly why there is so much excitement -- because there is a lot to discover, and a lot of progress that can be made quickly.
I agree with the author that fundamental physical and geometric approaches are still relevant and useful, and have been somewhat ignored recently, but the fact remains: If you and I as individuals want to maximize our personal impact, and capture as much value as we can while working on interesting problems, deep learning is an excellent field in which to do that.
It's kind of like we just discovered a nice vein of gold, and the silver miners are like "yeah, but we don't know much about that vein of gold and how long it will last." Which is true, but in the meantime, there's a lot of easy money to be made, and ultimately, both types of resources are important and synergistic.