Ah that's a game I've been meaning to get into.
On their website and forums they'll explain how you can go about changing assets or make your own. Actually looking at their documentation it's pretty complete already and there's a section on modifying game assets. Look for the file HACKING.gz in your usr/share/doc/freeciv-data directory.
>Currently the graphics is stored in the PNG file format (other formats
may be readable by some clients).
But the issue in your post has to do with file permissions. Either look into how the file permission system works on Linux based systems or try man chmod if you feel like reading technical gobbledygook on this. All you'd need to do is run the command as root while opening them with GIMP or run a command as root to change the permissions of the files. It's a security mechanism that's outdated and designed for multiuser systems but it works and isn't too much hassle to learn either.