For what it's worth, I'd say that most of the warnings in this article don't really apply until after your first year or two (though it certainly varies a lot between different schools and different fields). If you're in your second semester of a PhD program, you've gotten a taste of grad school, but almost by definition you haven't had time to hit the "my last year's worth of work went nowhere" point discussed here, for example. Heck, if you're in the USA you're probably still taking classes at this point.

Maybe your experience will continue to be mostly positive, but I don't think you'll be in a position to really judge this article for at least a couple more years.