Hi Siddharth! Hope you're well -- let's break down this quote.
Darwin writes: “The question of whether there exists a Creator and Ruler of the Universe has been answered in the affirmative by some of the highest intellects that have ever existed.”
1) “The question of whether there exists a Creator and Ruler of the Universe"
Put simply, this means: the question of whether there is a God, whether something higher created the universe (and continues to "rule" over it)... so it means whether God exists and whether God is still around + part of everything.
2) "has been answered in the affirmative" -- the question of whether God exists has been answered "Yes." (aka yes, God exists)
3) "by some of the highest intellects that have ever existed" -- and smart people in history are the ones who believe God exists (and smart people are experts at these kinds of things).
So, put together: The question of whether God exists has been answered yes by the smartest people through history.
Even simpler: The smartest people to ever live believe God exists.
This is important because Darwin came up with the theory of natural selection aka evolution, which many have taken to believe that the creation of the world could be explained through science. Here, Darwin is at least saying the most intelligent people in history all agree God created the universe (and rules over the universe), making things a bit more complicated. For example: Is God a part of science? Does God work through science and natural selection? Perhaps Darwin thinks so!
It becomes especially interesting when you think about schools in America and around the world banning the teaching of evolution because it's "atheistic." Here, Darwin seems to suggest God has a hand in evolutionary biology.
Hope this helps!!!