I just started playing this game again after a year+ break, so I started a new game. Anyway one of my first captives is this girl who has the trait 'Likes It Rough' which says: "Rape actions cause no loyalty and obediance reduction"

So I think... okay, I can just have sex with her without all the chatting/hugging/whatever right? So I try that, but alas, whether it is rape or if you convince her to be intimate, either way when it gets to the sex scene every action will result in "She resists by brute force" any action, for every action until it is over.

And then... the cherry on top, is that every single rejection results in huge obedience loss, so she goes from green to red in one sex act. Even if she agreed to do it! How does this make sense? 

I am guessing the source of all this is the "Due to recent events Daysi rebels against your control" in red under her profile, which seems to be a thing for all new captives. However is it me or is this totally inconsistent with the purpose of the trait, "Likes It Rough"? 

Is it just a boring waiting game? I have to wait 1 week+ for every new captive to do anything? How the hell does a slave in jail even resist rape by brute force anyway? I don't understand it at all lol. 

After playing it with some more, I am no less baffled by this "Due to recent events X is rebelling" buff. Why the heck is this even in the game? Its only purpose seems to be to deadlock your progress with girls, which in the beginning is really slow. You can't have sex with your own sex slaves in jail. What IS that!?  It's just insane. Am I supposed to get a written contract of consensual sex from them? WTF? Did I download "Strive For Power - Feminist Edition" by accident? A petite fairy with 0 strength in prison can "brute force" resist the 6 str man who has her chained in prison? I know this is a fantasy game but get real! 
The whole sex system seems to work similar to the Era games (Eratohok, tw), except for this notable exception, there wasn't any bullshit where you just had to wait a month before doing anything to them, probably because it's insanely stupid and seems almost intentionally counterproductive to the point of a slave trainer game.
Probably the best part is where traits don't actually mean anything, because both "likes it rough" and "masochist" traits both hate being forced to do anything, or being hit, so long as they are rebelling, literally the direct opposite of the traits defining purpose. 

Sex in Strive is a steaming hot mess, and I'm talking about the code not the content. Much of it does not work as you may expect, or is clunky and hard to understand. It hasn't been fixed yet because it is a huge system that was halfway between converting to a new system when someone abandoned it.

That said, your problems are mostly addressed by Leonais. "Likes it rough" and "Masochist" are not free passes to do whatever you want, but they do make it easier for the slave to enjoy sex. Though unless you know the exact mechanics, I doubt that you will make use of them. The wiki is a bit out of date, but if you check the Traits page, it should give you a better idea of how they affect sex.

Edit: Forcibly raping my slaves into obedience and stopping their resistance is my early game play style, so except for the fact that male and female are basically equals this game doesn't qualify as feminist. Rape, torture, kill; just remember that the game has bugs. Speaking of which, I have a bugfix v4a that is released through Discord(https://itch.io/t/284398/discord) just use the search bar to find "change log", or use the older version here https://itch.io/t/667993/leos-mod.

I  actually think that the sex system is somewhat advanced compared to similar games out there - just discovered this game last week and really enjoy it so far. 

I had a similar problem with one of my slaves - she had full loyalty and she was getting a lust warning message. Sex was initiated through consent, but because she also was uncivilised, she resisted with brute force, as obedience is still less than 80 at that stage. 

Now that does not make any sense to me at all, but neither does female logic haha