Q: Do Anti-Doom points negate Doom points on a 1:1 basis?

…so that it would take three cards with one Anti-Doom each to completely negate the three Doom on, say, Cthulhu?

A: Yes. Anti-Doom and Doom cancel each other out on a 1:1 basis, both when counting up a given players Doom count, and when totaling the Doom count for the table.