Good q
We have come of age in our evolutionary process. We are past evolution as a species now. We don't act on natural instinct, in the sense that our empathy can outweigh basic, animalistic desires... like exiling a blind cousin through natural selection.
If we have a disadvantage, we can invent. You have to look at the human species in a way, that our brain is essentially the human, and our body is the evolved tool. Now, our evolution is on another tier from biological to technological. Instead of taking a mass amount of time to evolve x trait to solve y problem, we can, in less time, build n tool to solve y problem.
In Freud's quote, he is essentially saying, religion was there when we needed it, to grow as man. It taught us morality, and answered curious questions that we couldn't answer scientifically. Now that we have come of age, to understand that Zeus isn't pissed when we have a lightning storm and have a set in stone sense of morality, religion can only hold us back be keeping us ignorant to truth.