Board Thread:General Discussion/@comment-28032065-20160817092833/@comment-29690476-20160820064207

The conflict of human and monster is clear: Monsters, though way weaker than humans, have the potential to become powerful after absorbing one human soul. Humans fear such potential, thus declared war. Chara might also fear such power, in case some human give soul to a monster(if they are threatened to death) and stop their plan, whatever it is. Killing all monsters sounds reasonable to eliminate such possibility.

Or Chara is simply angry about being betrayed by Asriel (Their previous plan failed because Asriel didn't want to cooperate) and consider all monsters unreliable.

As the game implied, Chara prefers killing to solve problems. These reasons are strong enough for them to kill all monsters.