Most of them are acquired from missions.
Viewing post in Lust Odyssey (NSFW Visual Novel) comments
yeah, I maaaay have missed the whole missions mechanic xD
Now, I'm trying to get my crew members to actually do missions since their compliance is negative.
I'm doing a submissive playthrough, does negative respect affect that? I can't do any missions currently, since all of my crew members refuse to do missions.
Yeah, it is difficult to do missions with negative respect. Definitely possible though; I managed it. You'll have to have sex with Rylan and/or Feraldo (once each per day and you must sleep to reset it) to get compliance (it will become 2 immediately regardless of current value) until you can afford enough upgrades to increase everyone's compliance. Even then, it's possible not everyone will have above 0. It's a bit awkward because you aren't going to have much use for the extra resources by the time they become easy to acquire, but there are plenty of games that work that way normally.
I believe the dev is planning to add more people to the list of possibilities for sex for compliance, but I can't confirm that, nor do I know when if he is.