Publication means peer-reviewed and scholarly. Yes, a publication in Nature, Cell, Science, NEJM, etc. opens doors, but so do publications in discipline specific journals (like JACS). What matters is that one's papers be read and cited.

The system is far from perfect, but I don't think you'll find anyone in academia saying otherwise. I think of it being like Churchill's quote about democracy being the worst form of government, except for all the others that were tried.