Of course, in the best of all possible worlds, you'll end up with a perfect abstraction layer which is powerful enough to allow you to do everything you need, while hiding all of the the gory details. In the worst case, you end up with a leaky abstraction. Suddenly you need to know not only the underlying language, but also how the compiler works.
That's not to say that all abstraction layers are evil. C vs. machine code is an example of an abstraction that works well. You rarely need to dive down into the machine code and you can, to a large extent, be ignorant of how the compiler works and still be able to be a decent C programmer.
There's no doubt that developing for the web can be quite hairy and sometimes you wish you didn't have to deal with all of the compatibility issues etc. It's possible that the solution is something like Vaadin, which lets you develop web applications as if they were Java desktop applications. But I'm not convinced just yet.
I guess the real question is, what exactly is the problem with HTML? If the problem is that HTML isn't abstract enough, then yes, an abstraction layer would be the answer. But if the problem is something else then slapping an extra layer of complexity on top of HTML won't magically solve those problems.