Well, now that's a meatier point. I'd say there are natural limits to tolerance.
One is under no obligation to tolerate racism, for example. One may choose to be a friend to a racist in the hopes of being a positive influence, but this may be difficult for a person to manage without sacrificing their integrity. It must not be expected or mandatory. (And certainly not for members of the race being vilified.)
Similarly, a gay man may choose to be a friend to bigoted religious person in the hopes of opening their eyes to love, but this requires self-abasement of a kind that must not be expected and mandatory.
It's hard to figure out a system of tolerance for the intolerant, and it's not at all clear why they should get the privilege of being intolerant of others, and demand tolerance of themselves. This is effectively what we end up with in practice around religion, though.