It is neither arrogance nor a failure to comprehend the strength of his opponent.
On the contrary, as the deity who once transformed herself to seduce Theseus, Aphrodite was acutely aware of his strength.
Excellent martial skills, firm will, strong beliefs— from the standpoint of mortals, Theseus was indeed very powerful; he had even reached the pinnacle that a mortal could normally attain under ordinary circumstances.
For such a man, those deities with similar powers who lived in luxury seemingly should have been unable to defeat him in the Mortal Realm—yet the Goddess of Beauty also knew very well from the mortal perspective that true invincibility did not exist here.
In the past, as the King of Athens, Theseus reclaimed the autonomous states internally, crushed the rebelling Aristocrats who had turned to other deities, and centralized the power into his own hands. Externally, he displayed undeniable dominance; even the incarnations of the gods had been defeated by his hand.