Because GOAT discussions are about more than just winning. Terry Bradshaw was a tremendous winner - great winning %, four SB titles. But he's not in the conversation for GOAT because he just wasn't a great passer. Good for his day but not GREAT. Certainly not GOAT level great.
Look at their career numbers:
Flacco: 61.7%, 38,245 yds, 6.4 ay/a, 212 td, 136 int, 84.1 rating
Rodgers: 64.8%, 42,944 yds, 8.1 ay/a, 338 td, 80 int, 103.1 rating
I mean, their passing numbers aren't even in the same universe. So GOAT conversations are about more than "just" winning. In order to be in that conversation, you need to be both a tremendous winner AND have tremendous numbers. Rodgers has both.
But this conversation is about *winning*, not *GOAT*. And there's no doubt that Rodgers has been a big-time winner. Not Brady-level winner, but a winner nonetheless. That's not really debatable.