Ah, Red Ninja.... I have several reasons for Kaoru and Enishi.
The first is that he is darned cute (naturally I want my favorite character to have a happy love life).
Another is that it seemed to make sense. All that time on the island, the way he started associating Kaoru with Tomoe towards the end, and all that. What with his sister complex, it wouldn't take much to drive that in a different emotional direction (hopefully he wouldn't continue to see her as his sister, though, ew)
Yet another reason is because as a tragic and broken character by the end, I felt he deserved some happiness. Kenshin is nice, but he is also very absorbed in his own mission and I wondered how happy a life of sacrifice would be for a character I enjoyed as much as Kaoru. I know she loved Kenshin, but he always seemed to love helping people more. He was devoted to causes, and Kaoru was willing to be second to that because she loved him. But that worked for them.
This way Kaoru gets someone who can be focused on her, whom she can actually help heal his emotional scars, and who can be delightfully sinister when you write for his character. (I like a little darkness in my male leads.)
If you really want to know more on why, I can go on, but I'm rambling now as it is and a little late for something.

Just had to attempt to answer your question, though. Oh yes, and I also like the Sano/Kaoru and Soujiro/Kaoru fics and even Aoshi/Kaoru, I just like seeing how she reacts to all these different personalities (who are all messed up in that series emotionally, but all very cute as well).