In The Matrix trilogy, few others aside from Neo are able to go toe-to-toe with the Agents, yet Morpheus is able to beat Neo early on in the first movie. Even with Neo growing into The One, Morpheus is able to take him on and defeat him multiple times, despite him later finding it impossible to defeat any one of the Agents he then comes up against. Neo and Morpheus are worlds apart in their power levels once Neo embraces his status as The One, but does Morpheus' victory here mean little against the Agents?
The Agents hold a fearsome reputation amongst the various crews and ships that traverse the Matrix itself, and rightly so. Their speed and brutality make them a combative force to be reckoned with, while their programming which drives them to kidnap captains and extract the codes to Zion's mainframe makes them a serious threat to all of humanity. If Neo is easily able to dispatch the Agents, as is shown towards the beginning of The Matrix Reloaded, why does Morpheus have such difficulty in facing them himself?
Morpheus is a formidable opponent and proves his mettle time and time again throughout the trilogy against a variety of enemies. Yet, when it comes to the Agents, Morpheus still cannot defeat them despite beating Neo previously. The obvious answer is that Neo is very much in his character arc infancy after being unplugged when he comes up against Morpheus as part of a sparring program in a digital dojo. However, there could be more behind Morpheus' lack of ability to defeat an Agent in a variety of subsequent scenes, despite his martial arts prowess.
All of the evidence from Morpheus himself suggests that no one has ever fought an Agent and lived to tell the tale, starting with his warning delivered to Neo during the training program with the woman in the red dress. It is here that Morpheus tells Neo he will be the first to defeat an Agent but then seems relatively unsurprised when he later asks Neo how he was beaten in the training program. This scene reveals a lot about Morpheus as a teacher to Neo and why he is able to defeat him with the knowledge he holds.
Prior to the fight starting, Morpheus explains to Neo that the Matrix is similar to a computer system in that it has rules like gravity, some of which can be bent and even broken. After repeatedly deflecting all of Neo's attempts to strike him, Morpheus asks Neo how he was beaten. Morpheus knows the rules of the Matrix are at his mercy, to an extent, and that the breaking of those rules determines whether or not he will succeed. Morpheus realizes Neo's potential limits far exceed his own, despite the rules of the Matrix itself. If it is as malleable as it seems, Morpheus may recognize his own lack of ability to break those rules in comparison to Neo.
At the point of the sparring program, Morpheus is merely pushing Neo to embrace this malleability to the environment around him while recognizing that he himself still falls short when it comes to fighting the Agents. Thus, when fighting Agent Smith in the hotel bathroom and Agent Johnson atop the trucks on the freeway, Morpheus is unable to beat the Agents given his own inability to overcome the rules in the same way Neo can. The obvious answer here is that Morpheus beats Neo because he is not yet The One, but there is greater nuance to Morpheus' actions. The sparring program is a lesson from Morpheus, one that helps to define Neo's journey towards becoming The One and the savior of The Matrix trilogy.
