Yes. But forward-consistency and early access are both valuable for site-makers, so pre-standardized features are prefixed in case they change when the standard comes out.
If you want to use standards, you need to select what's available to you by your target audience, and ignore the non-standard-compliant cases. If you want to do things, and keep as large a target audience as possible, you need to either hack them together with old tech or jump through hoops to do it with new tech. Especially given the web's rocky past, many developers would prefer to use the new stuff. And there are tools to help - Less or Scss, for instance, make those prefixes essentially free.
But that's just a fact of programming in general - you could write a web-app and get it on any computer with a modern browser. Or you could write it in Ruby, and get it on any computer with a Ruby interpreter, and include an installer / instructions for those that don't. Or you could write it in C, and get it on any computer with a C compiler, and you may have to write your own library code / preprocessor controls to handle strange architectures, and change things based on your target OS. Or you could write it in assembly, and have it run on almost anything, but have to handle multiple flavors and an endless variety of available memory, and input and output devices.
Or do any of the above, pick a subset of the devices that are technically capable of reading your code, and screw the rest. Porting Doom 3 to Commodore 64 probably isn't going to work, despite the code being written to the standard of whatever language it was written in (probably C, which I will assume for now), and compilers adhering to the same standard for targeting the C64. That you can't run Doom 3 on your C64 doesn't mean the standard is broken or useless.
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The nice thing about those prefixes is that, in general, it means you can use new features and know they'll work as you designed for years to come. If a re-design every year or so is cheaper than vendor prefixes, then yes, they're a pain - wait until the standard comes out. If not, they're a time saver to get handy new features a couple years early, and free switch-over to the standard when and where it's implemented.