This a textbook case of Chesterton's fence: before tearing down a fence, find out why it was put up.
This fence went up because plenty of people never figured out how to enable launch at login, kept missing their notifications, and let us know they weren't happy about it. So on-by-default is what causes the fewest headaches. It's also one click to turn off.
Hanlon's razor says never attribute to malice what's adequately explained by stupidity. In this case it isn't even stupidity, unless listening to user feedback counts. Can't make everyone happy!
That said, I'd be happy to implement a setup step on first launch where you choose this upfront. Have a triply nice day!
The comparrison with Steam is actually helpful, since the Steam client itself is by default set to auto start as well, with an opt-out option for those that don't want it. This is done for the same reason that Fluxer also has auto start enabled by default. (There is also a huge differnce between a game, something you usually don't keep open in the backround, and a chat platform, something you do usually keep open in the backround to get notifications.)
Default behaviour should in most cases be set to what most people want. In this case it most likely is opt-out although that isn't certain unless Fluxer starts doing A/B-Testing (which i hope doesn't happen).
That said, putting this option in the setup wizard for the desktop app wouldn't hurt imo.
Thread
Comment by Hampus
Comment by @SteveLinkNoah