Because Pubky is both protocol and an app. Nostr use cases are actually a subset of Pubky's, not the reverse, because Pubky also introduces discovery via PKDNS.
Discussion
That makes thing even more complicated. Using the same name for the protocol and an app… Why?
I think Pubky has a marketing problem there (yea Nostr has marketing problems too).
The mktg problem you describe appears to simply be that Nostr people are not interested in other technologies, to the point where they will invent reasons to hate them and speak badly of them, while knowing nothing about them at all.
Real users of apps don't care what the protocols are called.
Real users of protocols don't care what the apps are called.
Neither of them genuinely cares if they are the same name.