>>3719019>>3718547I don't think Rei ever felt jealous of Shinji. Gendo was pretty horrible to Rei and she didn't know any better thus far. So, when Shinji shows a little bit of human decency and genuine care towards her, she instantly starts questioning both the nature of her relationship with Gendo (which is one of the most fucked up things in the whole EVA) and her own purpose and existence. Not that Shinji did much, actually, he could have done so much more for Rei hadn't he been so psychologically crippled (nor distracted by Asuka). But even that tiny bit was enough for her to start to grow and go astray from Gendo.
On the other hand, Shinji is definitely jealous of Rei. Not for the actual Rei-Gendo relationship, but because of what he perceives as that. His perception is of course, marred by the projection of his inner fears, but that doesn't stop him having conflicting feelings which may have partially played a role in his not reaching out more for Rei.