Disclaimer: I am cynical, and an evolutionist.
I am inclined to believe the opposite is true. Tolerance is a learned behaviour, and intolerance is a natural human response. I think intolerance is a side effect of natural grouping behaviours which served their purposes long ago. Humanity’s laudable widespread efforts to eradicate intolerance; the acceptance that all people are born equal; and that those of other race and gender should have the same opportunities is an extremely new concept, when looking at the grand history of the human race.
Before the arrival of organised society, grouping had a powerful function. People who looked and acted alike would form clusters of protection for each other, and within that group, hierarchies would naturally form based on various aptitudes, in order to best protect the unit from outside dangers – be they natural forces or other humans.
When humans begin forming massive organisational structures, it became impossible to know all of the individuals within a unit, yet we were expected to accept these all as part of the group. This was less difficult in ancient times, when civilisations were formed around similar individuals, and belief systems were imposed upon the population by force. Modern society opened up the ability for a civilisation to be formed of many different “types” of people. Additionally, as the “group” became more and more massive, the human mind began to form artificial differences between groups that would otherwise have been considered “like” in older days. Sub-cultures erupted, and a natural fear/loathing between them took hold.
We are all now taught at an early age to accept others, no matter what they look like or believe in, but this is a psychological imposition on a biological system which is still not geared toward that. It takes effort to be accepting of everyone you see, depending upon how well you have learned to be accepting. Some do not find it difficult at all, while others who grew up in areas that still feature segregation and prejudice might have a hard time adjusting to tolerance. Some might go there whole lives struggling with it.
So in that light, the objection you noted is a positive sign that this learned tolerance is strong enough to overcome the intolerance of those who were never taught to be tolerant.
What is natural to civilised society, and what is expected are two different things; one could even say opposing forces. Our nature is still rooted in many tens of thousands of years biological evolution. Civilisation could be seen as our conscious, psychological effort to overcome to the tribal mindset. It is a testament to the collective willpower, and any failings on a micro and macro scale within any civilisation are a testament to the inherit weaknesses. These forces are self-serving. A tolerant society breeds tolerance from generation to generation, while an intolerant society can breed the opposite and create a tendency for empire aspiration and insularity.