It was originally a Street Fighter move. Gouki/Akuma used it first, then Capcom pulled a SF on X4 by turning Magmard Dragoon into Gouki, adding Drop Kick, Hadouken, Shoryuken and other things in there.
This made it so that X would be Ryu, Zero would be Ken and Sigma would be Vega/Bison.
Zero got SF moves in later games, X8 being the latest, where you could do Shoryuken, Tatsu Maki Senpuu Kyaku and the Flame Kick. More noticable if wearing the knuckles. It's the same for Layer. X got Hadouken in X1 and Shoryuken in X2. Too bad Tatsu Maku Senpuu Kyaku wasn't in X3, but the Gold Armor was neat too. ^^
So yea, Street Fighter was the reason for Zero's Flame Kick. Probably for fan service, but also because both X8 and IHX were 2.5D, the Capcom team were able to give that move to Zero more easily that way. ^^ </wii>