Society has to constantly make trade-offs between competing dangers from both sides. On the one hand, there is the danger of initially innocent behaviour escalating to harassment and violence. On the other hand there is the danger of people being punished for entirely legal and non-violent behaviour and speech that other people find offensive, disagreeable, or politically heretical. History provides many examples, where society tells its citizens "You can't say that!" and the those societies are rarely, in retrospect, ever considered to be the good guys. You say "It is clear to me, from my own observations and from my own experience as a male, how attitudes develop from seeds of thoughts and behaviours at very early ages," and exactly the same is true of authoritarian politics. If children learn that it is OK to use the power of the authorities (parental, school, or government) to stop other people doing things they don't like, but which are not actually themselves harmful, then that behaviour escalates too.
We all do things that other people don't like. We all hold opinions other people don't agree with. And while we all think wouldn't it be great if we could stop other people doing all those things that annoy us, once you have established the principle that it is OK to do that, then other people get to do it to us. We will not always be in power. And that's not so much fun. "Tolerance" only of things that don't offend us or annoy us is meaningless.
Liberal and tolerant societies usually adhere to some variant on JS Mill's Harm Principle - that the only justification for society to intervene in any individual's freedom of action is to prevent actual harm being done to others without their consent. And it's important for children to learn where the boundaries are. A boy who wolf-whistles, intending only to say "You're amazingly beautiful!", is not doing any harm. Intolerance of behaviour that is irritating but does no harm teaches the wrong lesson to both the boys and girls about the sort of society we all want to live in.
You don't give any indication your daughter was upset, and if she's not then you probably don't particularly want to distress her by telling her that this is dangerous or she ought to be offended when it's not intended that way. That could frighten her unnecessarily, induce an emotionally damaging fear of the opposite sex, or create actual hostility and conflict between classmates. It could also tip the boy's attitude from fun into actual active hostility, if they feel they are being punished unfairly. (The boy's friends and family, too.) And all children should be aware that other people are allowed to be culturally different, and to do things that might annoy or irritate us, but which so long as they do no harm are to be tolerated. On the other hand, they should also know what to do if it does escalate to credible threats of actual harm, and that they are not expected to put up with that.
So I would suggest this is a situation to keep an eye on - just to make sure it is not escalating into anything more dangerous - but to be clear that this is a case of a cultural difference to be tolerated. You might ask whether the boys are doing it in her presence, and whether it bothers her, but I'd not make a big deal of it.
And on the topic of how attitudes develop from seeds of thoughts and behaviours at very early ages, we might want to reflect on the research that suggests sexual violence arises more often from childhood repression of sexual behaviour, making it something dirty or forbidden, something to hide and be ashamed of. Boys who grow up believing that girls don't want to be admired or approached, and will always reject them, or that any attempt to initiate things with a girl will result in them being stamped on by society, are the ones most likely to seek less civilised alternatives and take it by force. The starving are the ones most tempted to steal a loaf. So the best way to avoid trouble is to make sure there is a well-marked pathway by which boys can meet girls in a way that's safe and comfortable for all parties. Don't just tell the boys 'No, that's wrong'; make sure they know what they ought to do to do it right. Five is way too young for the birds and the bees, of course, but it's not too young to be introduced to appropriate ways to get on friendly terms with the opposite sex, with tolerance for their many exotic cultural differences!
