And Cryptonote is not "another popular coin." Cryptnote is a family of popular coins, most of which greatly exceed XCN in volume.
Exactly, there isn't even a coin called Cryptonote, they just use Cryptonote technology. So we have some algorithms which might be confused with our coin, I don't see why that's so bad.
I know, let's change the name to BiteKoin. It's spelled different, so nobody except imbeciles could possible confuse us with ByteCoin!

BiteKoin would be pronounced exactly the same way as ByteCoin, and in that case I do see an issue. But there is no other coin pronounced exactly like Cryptonite so it's harder to confuse.