Usually that advice isn't badly intentioned but just because people are used to doing things that way. Just as an example, if you download a package or something even if you could use GDebi Package installer to install it with the gui, every tutorial you ever see will probably tell you do `sudo dpkg -i` or something. Nearly every Linux problem a 'regular' user is likely to have falls into this category - there's probably a semi-sane way to do it with the GUI, but everyone who uses Linux will think it's 10x easier to just give someone a command instead of clicking through some lengthy graphical process.