To be intolerant of intolerance is one of the cornerstones of liberal thought. Karl Popper was the first person to explicitly outline the philosophical justification for it, but the reasoning is really quite simple. Liberalism is not an ideology that preaches that all ideas are of equal value, it explicitly privileges what it defines as the moral concepts of liberty, equality and virtue above other ideas. It is a 'universalist' ideology because it refuses to accept that their is any possible justification for illiberal ideas, for example the idea women should be restricted on the basis of their sex or that people should be persecuted for religious faith. What people advance when they say that the intolerant should be tolerated is a more relativistic argument that I think stems from particularist multiculturalism, where all ideas are put on an egalitarian spectrum to the point where criticising another culture's beliefs is impossible and undesirable.
Of course everyone should have the right to speak their mind, but everyone else has the right to treat others differently based on what they say; and in a healthy, moral, and liberal society those who are intolerant and disruptive should be frowned upon, whilst those who are tolerant and respectful of the rights of others should not.
Antifa were by far the small majority in those protests.
I don't see what is 'bigoted' against what they were protesting against though. They were opposing the collusion of major capitalist world governments for various reasons. They used violence, but this does not necessarily mean they are 'bigoted'. The third estate wasn't 'bigoted' for revolting against a feudalistic aristocratic monarchy, for example.