You’re conflating two things. Yes, the EP CAN reject. In practice, it rarely ever DOES.
How the democratic process actually works is important. Public outcry often happens after something becomes LOCAL law (i.e. a few years or months down the road) implemented in a member state. The usual defense from EU-enthusiasts is then “you should have engaged in public debate, it’s too late now”. That should tell you something about the visibility and publicity of the process.