The underlying user/group systems are a little more secure, containerization is common and easy (flatpak, bubblewrap, and firejail), the attack surface is lower, the marketshare is smaller, and repositories are fundamentally superior. Of these, app repositories and the market share are by far the biggest factors.
Getting malware on Linux isn't totally unheard of, but it is extremely uncommon. I've never had any, nor has anyone I know. This guy isn't the first person I've heard of getting malware on Linux, but he is one of very, very few.