If someone is using Tor, it doesn't mean that they are some l33t cypherpunks, it's likely just people who want to buy drugs online, and use that browser because that's the only way to access .onion sites.
but not always
I run my own .onion domain, you know why? Nothing nefarious, it's just easier to set up an addressable IP that way. I can login to my Raspberry Pi remotely using the .onion address, then check my lightning node, manage it, or (only in rare cases for now) use it to pay for something.
asking your ISP to give you a static IP to use and configuring it through a router is not such a great option; if you change to a new ISP (or just move to a new place), it all has to be set up again. A .onion domain you can setup in about 5 minutes (less really), and you can take it anywhere without having to go through a whole load of bs. Bitcoin's gonna be supporting I2P and CJDNS sometime soon (and so hopefully Lightning will too). Those 2 are better tech than Tor in many ways, and you can use them just as easily to set up a reachable IP.
so using Tor can easily have nothing at all to do with anonymity (Lightning is designed to be anonymized whether you use it over Tor or not), it's simply a case of practicality for me.