"It was Sigmund Freud who suggested that history had given three insupportable blows to human self-esteem. The first was the revelation that the Earth was not the centre of the universe after all. The second was Darwin's: that humans were just one more species of animal. The third, Freud modestly suggested, was his own work, which robbed humans even of the consolation that we at least possessed rational minds."

That human tends not to be rational is hardly something Freud discovered. Now, it may be that no human can be as rational as they would like to think of themselves as being.
But only a very small minority of human ever imagined, let alone assumed, that rationality was a given or an absolute attainable. It basically was a fad like bell bottom jeans- though not as widespread.

Now, self-esteem as the word implies is something to do with the Self. If one lowers the value of institution or groups, a human can be capable seeing this as an elevation of the self. And a recent age called the Me Generation, seems to suggest that "self-esteem" hasn't been threatened in any way by such historical ideas.

As for the "center of the universe idea", aren't there still quite a few people which hold to the idea of our uniqueness? Rare earth? The idea the beginning life was lucky chance? Etc.

The world didn't really change much from these basic ideas- technology [and lot's little ideas] probably has changed the human and human thought far more.
Though the esteem that people regards there fellow humans may changed in a general way. For instance, considering our capability due to technology, the modern world seems rather indifference to the plight of the vast majority of humans living on this planet.
And extreme acts such as genocide seems to move people little towards action. One could offer many explanations for this, but self-esteem not connected to humans in general could one element of this.

But the simple undeniable fact is that the human as far as we know at the present, from all available evidence [rather than theoretical models] is an unique creation.

That we share our bloodlines with apes, pigs, dogs, rats and cats [or any known life form on this planet] doesn't change this is anyway.
People in the East, generally regard that there not just a genetic similarity connection, but a spiritual relationship and connection with all life [now, that can lead them to all kinds of foolish and idiotic ideas- I'm just pointing out it's not all human ideas being altered].

But my point is that the human is a godlike creature. But just because, human is godlike it does not follow that we need to establish some kind of caste system or belittle other creatures in this world- it's simply evident and is a fact at this moment.

Now, as for Progress. Again only a small number of humans ever held such an all embracing idea- that we part of some cosmic parade building toward utter perfection in all aspects. There were probably more Nazis than the number people who ever held such an idea.
If the idea is restricted to a perfection of the soul or going to some heaven, then you have much more significant number of people holding such beliefs.
And in terms of technology there is an obvious progress: we are flying around in the sky- and that has never been done before. Not to mention space exploration.

So, Charles Darwin and Freud did have a significant affect upon of culture, and much of the bad consequences that humans did can't be blamed on these scientists trying grapple with understanding our world and publishing their views. They were honorable people.

Unlike a not insignificant number persons far less honorable [murderers, thieves, liars, etc] but nevertheless given as much or more praise AND given political power- who only measurable lasting result was vast "blows to human self-esteem".