You gotta remember how SEELE played him at that moment, and they did a very good job of it as well. Using Rei's 'sister' was an effective ploy to get past Ikari The Younger's defense. You see, while a bit weak willed, Shinji is one of those people who gives a damn about other people - just not himself as much, unfortunately.

Also, remember that SEELE hunted him down, not the other way around.

So, once Shinji as some half-way decent experiences piloting an Evangelion, it only becomes natural that he readily takes that particular weapon into hand when he gets fed up and decides to do something about the situation.

Black Aeronaut Technologies Creative aerospace solutions for the discerning spacer "To the commissary we should go," Yoda declared firmly. "News of this kind a danish requires."