DOM implementations have had vast improvements over the past years, vendors these days are working on nanosecond improvements to DOM operations. "The DOM is slow" usually refers to design problems that can't be optimized away, like being 99% synchronous, exposing APIs that invalidate layout at arbitrary times, etc. So yes, a fundamental problem that was exacerbated by the incredible advancement of JS engines over the last few years, causing developers to build more and more complicated web apps.

To be honest, the fact that the DOM is as good as it is today is very impressive to me, considering how old it is and how much the landscape has changed.