I've yet to meet the person who was a programming god in trendy-language-of-the-day, but couldn't use a command line (perhaps with a few weeks' practice to change shells / operating systems). Maybe it's more to do with off-shoring, but whenever I see "programmers" who can only use a GUI, I know I'm in for trouble, and said "programmer" won't actually be good at issuing orders as lines of text for the computer to follow.
Yes, please give me cave paintings and tally marks! Don't make me learn stuff like functions, sets, pipelines or language!
A more valid criticism would have been "some programs/utilities/packages are more complicated than strictly necessary", with examples. Others have pointed out that it should be possible to make a "distribution" of a tool suite (perhaps as simple as a script containing the individual setup commands), rather than making every student run every step by themselves.
Having an "install" clicky thing from a 3rd party that has no options and just works is great. As long as that 3rd party knows all your needs (really knows, not the Apple mind control illusion) and has control of the environment in which you are dropping the package.