I don't remember people complaining when Robert Wise and the art and production designers updated the Enterprise, from the design aesthetic of what the "future" might look like to people living in the mid 60s to what the "future" might look like for people living at the end of the 70s.
By comparison, there has been an even greater span of time between the production of Alien and now Prometheus. Our technological culture has changed much more radically in the last 30 plus years, versus the time between TOS Star Trek and TMP.
I have no problem whatsoever with Ridley re-imagining the design aethetics, in light of the technological revolutions that have already occured, and extrapolating into the future.
The problems occur when you go in the other direction. Kubrick was a brilliant visionary, and simply nailed the "future-tech" that is presented in "2001: A Space Odyssey". Not only did he foresee the use of 3-D computer graphics (used in the various spacecrafts cockpits for navigation and docking), but they friggin' had flat screen displays. Heck, Poole and Bowman had iPad like devices on the Discovery. Yet, for some incomprehensible reason, in "2010: The Year We Make Contact", they have regressed to using old CRT monitors. I always hated that.