I want to read a manga with a male love interest that has red hair. I don't mind if the romance is a subplot as long as it actually goes somewhere. For example, the romance in InuYasha is a subplot because the main plot has more action involved in it. The romance in Inuyasha actually goes somewhere as well. I don't care what other elements are present in the manga as long as it has some romance. The manga I'm looking for has to have the love interests end up together.

Most red haired manga characters seem to be female. The few male characters I can remember don't often end up with the girl. (If you'd like me to recommend the ones with minor male characters I can, though). And you've read the first three manga I thought of (Fruits Basket, Rurouni Kenshin, and Futari no Renai Shoka).

A Stranger in My House - the male lead has red hair. It's a webtoon. I haven't finished it yet, but it seems like it will have a happy ending.

My Beautiful World - the male lead has pink hair (which is commented on by others). I'm not sure if that's close enough to red for you. It's a romance webtoon with another plot that is of equal importance to the romance.

Golden Days - the love interest has red hair (which looks really natural compared to most manga red hair). It is a shounen ai (the romance plays a minor role in the plot but is definitely memorable), so I'm not sure if you would be interested. Also,

The ending of the romance is more complicated than ending up together or not.

One of the guys has red hair:
Barajou no Kiss
Short Cake Cake
Bokura no Himitsu.
Cherry Boy, That Girl (webtoon full color)
Dangsinman Molla! (webtoon full color)
Nijiiro Days (MIZUNO Minami)
I Love Yoo (webtoon full color)
http://www.webtoons.com/en/romance/i-love-yoo/list?title_no=986&page=2

The male lead has red hair:
Mermaid Boys
Honey (MEGURO Amu)

Neowa Neo Sai - male with orange hair (webtoon full color)

Gokusen

Hatsu Haru 🙂

My Secret Brother Although he's not the main male protagonist, he is the romantic lead for the female protagonist.

His hair is only red when it gets wet, in https://www.mangaupdates.com/series.html?id=19434 Kaizoku to Ningyo

Quote from Solunasky

His hair is only red when it gets wet, in https://www.mangaupdates.com/series.html?id=19434 Kaizoku to Ningyo

Kaizoku to ningyo isn't romance, though? Unless you've read ahead of the point where the scanlations stopped and know something I don't 😛

The male protagonist in Inochi Mijikashi, Koi seyo Furyou Shounen! has red hair.
The manga itself is a shoujo and not that outstanding.
However it is short and fits your description. 🙂

Gu Fang Bu Zi Shang has a red haired male lead, and a romantic mainplot.Unfortunatly it's on a hiatus cus of the mangaka for quit a long time now 🙁 , but if you are interested you can read it in novel adaptaion.

You don't need to read ahead, there's plenty of subtext. 😏

You should try the categories "Red Haired Male Lead" and "Red Haired Main Lead."

The manga Fukurousou Aki Arimasu falls under this category, as does Fruits Basket among others.

Kyoukai no Rinne

It also has an anime adaptation which is currently in its 3rd season.