You should go actually read what Popper said about the paradox of intolerance, instead of projecting your own interpretation onto it based upon your assumptions.
Edit: here, I'll do it for you:
"Unlimited tolerance must lead to the disappearance of tolerance. If we extend unlimited tolerance even to those who are intolerant, if we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them. — In this formulation, I do not imply, for instance, that we should always suppress the utterance of intolerant philosophies; as long as we can counter them by rational argument and keep them in check by public opinion, suppression would certainly be unwise. But we should claim the right to suppress them if necessary even by force; for it may easily turn out that they are not prepared to meet us on the level of rational argument, but begin by denouncing all argument; they may forbid their followers to listen to rational argument, because it is deceptive, and teach them to answer arguments by the use of their fists or pistols. We should therefore claim, in the name of tolerance, the right not to tolerate the intolerant."
Put more succinctly: one ought to reserve the right to not tolerate the intolerant without limit, but we should always err to engage with them on the level of rational argument. Once they claim that rational argument is no longer the field on which they want to argue, and violence is, the right we reserve is to counter with our own intolerance of that, through violence if necessary, even though that is contrary to our principles of never being intolerant (hence the paradox.)
So no, it doesn't mean you shouldn't tolerate intolerance. On the contrary, it means you should tolerate it as much as humanly possible, but not limitlessly. It's basically the inverse of what you and others claim it says. The paradox is the fact that unlimited tolerance of the intolerant is paradoxical, not that any tolerance of the intolerant is. People who use this paradox to try to suppress speech that isn't directly connected to violence, specifically, are actually sitting on the "intolerant" side of this argument, funny enough.