What did Elrond mean by telling the council "it is so ordered ..."?

Elrond is saying it was not chance but Providence that brought them all together.

To expand on Glorfindel's correct answer, let me explain the passage phrase by phrase. This is actually pretty important in terms of understanding Tolkien's theology of Middle-earth.

• That [what shall we do with the Ring] is the purpose for which you are called hither. Called, I say, though I have not called you to me, strangers from distant lands.

  Here he is saying that the diverse collection of travellers and representatives were called to Rivendell in order to take part in the Council of Elrond - but not called by Elrond himself. Then by whom?

• You have come and are here met, in this very nick of time, by chance as it may seem. Yet it is not so.

  Here he also discounts the possibility that they all came to Rivendell at the same time by pure chance. Even if it may seem like chance, it's not.

• Believe rather that it is so ordered that we, who sit here, and none others, must now find counsel for the peril of the world.

  This is the key point: Elrond says "it is so ordered" that the various people gathered together at that particular place and time should discuss together and decide the fate of the Ring and of Middle-earth.

Ordered by whom, then? In a real-world context, this would refer to the notion of divine providence. In Middle-earth, written by the devout Catholic Tolkien, the analogue of God is called Eru Ilúvatar, a supreme being who intervenes rarely but crucially in the affairs of the world. See also Who called and ordered the Council of Elrond?, a question on another site inspired by the same quote that you're asking about. Note that the answers to that question don't confirm for sure that it was Eru Ilúvatar who called them all to Rivendell - it could have been a lesser immortal such as the Valar. I don't think this is ever explicitly addressed in canon material such as Tolkien's letters, and I don't know Tolkien's theology well enough to be sure if it was definitely supposed to be Eru Ilúvatar.

Per When did Eru interfere in Arda directly?, there were a few times during the course of The Lord of the Rings when Eru Ilúvatar intervened directly in the world, notably bringing Gandalf back from the dead and tripping Gollum into the volcano. For him to intervene in bringing all those people to Rivendell at the right time to form the Council of Elrond certainly seems plausible. (Note also that Tolkien tends to talk about this stuff very indirectly, as you can see from the quotes in the posts linked above. He doesn't come right out and say "Eru is God, and He did this or that", but uses euphemisms and suggestive language to make it clear.)