After accepting the reality of being raped by a woman, a reformed demigod assassin tries to deal with his depression by getting back into the business of hunting people who bear the Chimera Mark.

Hi
I think the story's goal and theme are revenge and justice. Who and how can be plugged in to support the goal and theme.

A mythological assassin strikes back to right the wrongs of rape and injustice...

This tells me he's a demigod and he's got some good reasons to pick up his assassin skills again. But it's still not enough info. Maybe what's missing is who is responsible for the injustice. You said a woman and a chimera mark. Is it an all women warrior civilization?

The concept in this logline is composed of too many unrelated events, odd descriptions and vague plot elements, for example;
Being raped doesn't necessarily, in most people's minds, make the victim want to become an assassin or become one again.
According to what most people think a demigod is, it is hard to conceive of one being raped and made a victim.
Finding new meaning is not a visual, objective and outer goal for a main character, it could be an inner goal but a logline needs to focus on the outer journey that drives the plot i.e the outer goal.

In short I think this concept has many logic flaws, and?to make sense of the story it require too much explaining?for a logline. Your explanations above essentially call for the reader to stretch their imagination to make up for what the logline can't deliver on, this is not recommended and usually indicative of a flawed concept.

Even if the logline is for a book, the core plot should still be able to fit with in the paradigm of a logline - a story is a story regardless the medium after all.

It's a very complicated story(it's actually a novel but I figured a logline would help me). Because I'm trying to keep it simple I've left out some important things about the world. Chimeras are people who started developing powers about ten years ago(including demigods and mutants), and then two years ago all chimeras developed a mark on their body that would identify them as a chimera. Due some actions done by a few chimeras, the world now sees them all as terrorists, and lynchings and racial profling and a whole lot stuff goes on.
So there are a few elements I could include in the logline:
The rape(His trying to deal with it is the actual inciting incident of the story)
The backstory. (Anti-chimera populace)
Assassin(He turns back to his old profession, but it isn't a very big part of the story and is quickly dropped, though his penchant for killing stays throughout the novel)
There is no person that is an antagonist until later, but he?faces man vs society, and man vs self conflict until an antagonist arises.
Goal(To learn about the mark and also why chimeras only started appearing ten years ago.)
So, to keep it short I could cut out the rape, which I'm hesitant to do since it is an inciting incident and a very defining and intriguing part of his character , and then focus on the backstory.
Or perhaps I could try to think of another goal to focus on.
For the 3rd revision I'm going to try focusing on the depression. (I hadn't planned this part but it is a part of depression so it fits to add it.)

Revision #3
After being raped, a suicidal demigod tries to find new meaning in his life to deal with?his depression.