Please first note that Noah Harari is not a scientist but a historian.
What does he mean by "intelligent design"?
Intelligent design is a set of fallacies invented by christian extremists to try to contradict a set of evidences that they have a hard time to include into their faith. Intelligent design has nothing to do with science. It is therefore impossible to state anything about this sentence except that it does not mean much.
However, from this quotation alone, one can't be sure that Noah Harari chose the term "Intelligent design" in reference to the commonly referred concept of intelligent design. He might have meant something else and might have tried to use some term that sounds sensational and poetic as talking about this book some have said that
the attractive features of the book are overwhelmed by carelessness, exaggeration and sensationalism. (see theguardian.com). My first feeling is that you could try to ask him (contact information are there)!
@tomd found this source which clarifies the author intention.
Not all people accept this idea. Religious fundamentalists insist that intelligent design rather than natural selection has shaped life on earth. They argue that the intelligent designs of a great god sculpted the long necks of giraffes, the colorful tails of peacocks, and the jumbo brains of humans. To the best of our scientific understanding, these religious zealots are completely mistaken. The past history of life owes nothing to divine intelligence. Ironically, however, the zealots may well be right about the future. Very soon, the four-billion-year-old regime of natural selection may be overthrown, and life in the universe will increasingly be shaped by the intelligent designs of divine beings. For in the medium future, we humans are likely to turn ourselves into godlike beings, possessing divine abilities of creation by design.
What I know is that natural selection is the main process that brings evolution.
Natural selection is one process yielding to evolution. There are other processes such as genetic drift. Stating
natural selection is the main process that brings evolution all depend upon what statistic of evolution you would like to consider. For example, you might want to know that most fixed genetic variation among species is due to neutral mutations (and therefore genetic drift) and not due to natural selection.
You might want to have a look at Understanding Evolution by UC Berkeley for a short introduction to evolutionary biology