Bayek is not the sole founder of the Assassin Brotherhood. He co-founded it with Aya. She changed her name to Amunet and founded a Hidden Ones chapter in Rome, where Bayek stayed and formed the Levantine Brotherhood in Egypt. Technically, neither was an Assassin, as we don't know when the order changed from the Hidden Ones to the Assassin Brotherhood. Maybe we'll find out in Valhalla.
Saying Aya is only remembered for killing Caesar and Cleopatra is utter nonsense. If that's the case, Ezio would only be remembered for killing the Borgias. It has nothing to do with Bayek keeping his kills under the radar, Aya (like Ezio, Connor and Darius) killed major figures that influenced world events. Bayek didn't. Darius also wasn't an Assassin/Hidden One, that's correct, but that's because the Order didn't exist yet. He's still immortalized with a statue beneath the Villa Auditore because of his contributions to not only the world, but the Assassins as well.
Darius invented the Hidden Blade, something we know was used all the way to the modern times as Desmond also wielded one. Aya founded the Order and had the higher profile kills, that's why she's remembered and not Bayek. These are the reasons Bayek is not remembered like other Assassins. Bayek is more along the lines of Achilles (Connor's mentor). He founded a chapter of the order but didn't really have major contributions otherwise.
Again, I like Bayek. He was a good man. But Aya was the more important of the two.