Which video game villains made sense on why they became a villain ?

Depends on what you mean. Do they make sense as a character, to do they make sense as in their actions are logical and/or justified?

Maybe Niko from Gta 4?

Bravely Default I guess going by pretty much what everyone who plays the game says. "It made sense why they became villans as opposed to being evil for the sake of being evil"

Because it's fun to play GTA in real life server.

Bowser, gotta get that woman with any means possible lol.

The Batman Games have at least some villains that fit your description

Caius from Final Fantasy XIII-2

Superman in Injustice: Gods Among Us.

Hugh Darrow (Deus Ex: Human Revolution),

Superman (Injustice: Gods Among Us),

The Stranger (The Walking Dead),

Karl Ernst Rasch (Crysis 3),

can't think of any more examples though. Oh, and The Dog from Silent Hill 2.

Andrew Ryan from Bioshock. He was a visionary, but he had to deal with psychotic murderers like Fontaine and dumb-ass lost kids that get back to the city and work for him thinking he'll help them :-p.

Hector Le Mans and Domino Hurley of Grim Fandango; one of the most common evils: taking advantage of other people to better their own situation in li-- err... in death.
GLaDOS in Portal/Portal 2: for science...? Maybe...? No... nevermind... she's just insane. But I think her insanity is justified.

Kefka was pretty good. I miss bad guys like that in video games now. Why can't the bad guy just be an insane sadistic asshole who wants to kill everything or become all powerful? inb4 the joker

Dagoth Ur from Morrowind :)
Darth Malak from KOTOR

Ganandorf from Legend of Zelda Ocarina of time. He just wanted to conquer the world. :P

This guy