Some problems:

• Stability. For me, Linux on a VM (where I'm using it for development and getting myself familiarized with it) was a stability nightmare. Everything could go wrong after an update (I'm looking at you, Ubuntu 24.04), or even a restart, with no easy way to recover.
• Lack of an easy recovery. On Windows, you can recover your OS from a faultry update easily. If a bit more things have gone wrong, just use the installer, to resurrect your own installation. On Linux, you're on your own, and while sometimes it's an easy fix, other times you're better off reinstalling your OS, leading you to have to restart a lot of other things, which leads to lost time that could have spent better with doing something productive. I've wasted hours on recovering data from a Ubuntu 24.04 installation which decided to no longer work in GUI mode, and it ultimately ruined my sleep schedule.
• A lot of settings are hidden deep within config files, which need manual editing, and even worse, googling, which on today's internet, will likely lead you to an AI generated site filled with garbage. I managed to kill the Linux installation on my Raspberry Pi, which lead me to the previous point of having to reinstall, then having to google even more settings because Raspberry Pi OS had the great idea in the newer versions to "make setup easier", thus tieing your location settings and your keyboard layout, so I had a Hungarian layout that I had to change, as it's horrible to use for software development (a lot of commonly used characters are on the Alt Gr layer, and there's only one Alt Gr key, the other Alt is a dedicated menu key - thanks IBM!).
• Production software and drivers. While Wine is fine for a lot of games, but try to use software with way more sophisticated copy protection schemes. They're already a pain to use on Windows with the original keys and such, now imagine them on a Windows emulator. Good luck with trying to find VST plugins, which copy protection can be 100% removed!

I'm not a good UX designer, but my first two rules for anything GUI related are:

1. If it can be done by a single button press, it should be a single button press on the GUI.
2. If it can be an easy configuration, it should be an easy configuration on the GUI.

Linux, alongside with many other projects in the FOSS community, regularly fail both of these, in favor of scripts, which are fine, but have their own issues. Your average user's average usecase does not involve "very repetitive tasks that are just perfect for some shell scripts".