True, Lucius disliked the Weasley family. Tom did not necessarily choose Ginny, just used the situation to his advantage.

Another reason, perhaps Riddle told him to pick the youngest (or female) of the Weasley family; because he would view her as the weakest or most vulnerable. This is due to Riddle's arrogant nature & he was able to manipulate her to trust him (especially when he learned of her crush on Harry).