The suffix ka 家, used in the word mangaka 漫画家, is actually used to name professions related to something. (the kanji is also used for the word "house," ie 家, but that has nothing to do with the meaning described in article)
Basically, the guy who works with manga 漫画 is a mangaka.漫画家. The guy who works with doujinshi 同人誌 is a doujinka 同人家. The guy who works with...
- geijutsu 芸術, "art"
Is an "artist," geijutsuka 芸術家
- shousetsu 小説, "novel"
Is a "novelist," shousetsuka 小説家
- ongaku 音楽, "music"
Is a "musician," ongakuka 音楽家
- shashin 写真, "photograph"
Is a "photographer," shashinka 写真家
- seiji 政治, "politics"
Is a "politician," seijika 政治家
- senmon 専門, "specialty"
Is a "specialist," senmonka 専門家
- hyouron 評論, "critics"
Is a "critic," hyouronka 評論家
- hatsumei 発明, "invention"
Is an "inventor," hatsumeika 発明家
And so on. That's how the word mangaka 漫画家 came to mean "manga author".
One thing, however, is that the usual word for "author" in Japanese is sakka 作家, which is someone that deals with the "works," saku 作, he creates.