The serpent represents many thing's, if you look at the hieroglyphs you will see the serpent on pharos head. The answer is mainly from Kabbala, the mystical realm of the mind in connection to the world.
I am not a professional, nor a Kabbalist, just one that prays.
From what I know, (articles, and such) the serpent is based from the kundalini, (the lower bone of the spine) Thats why we have to bow in tefila and make our spine like the snake (Gemara Kedushin daf lamed) if not you won't be resurrected when mashiach comes. The story with the seven headed serpent in the bait-midrash.
This being so, g_d works in secret ways, like a serpent he does not know what color is, nor what animals are, he just sees energy (Thats why he asks Adam ha rishon, "What do you see")
Again this is all connected with Energy and Mind manipulation, the alfa snake is one you must be careful as they can bite you and you will never recover, like the bite of the wise men.
you can also see a connection with a big Kabbalist, rabbi Abraham Abulafia, and three headed serpent that represents, christianity, judaism and islam. The three main (alfa) religions in the world, irrelevant of the size of the religion.
There's a story of Rabbi Zalman mutsafi Another great Kabbalist of the twentieth century, he was praying for the holocaust to stop, (along with rabbi ptaya, though they were not together, and rabbi ptaya did more things). during his prayer he was shown a serpent with metal fangs, and voice from behind the serpent said, him, "I recommend you to stop, no one can defeat this serpent, as a bite from this you won't recover) from then on, rabbi mutsafi stoped praying in relation to.
We see from here that Moshe was not afraid of the serpent only the hidden message it portrayed, that he was talking to a real diety, remember nowhere does it say that Moshe knew hashem before like he knew hime after, so you can presume, that his first encounter was that of an alien encounter, and not a mere mortal mind that he himself could defeat, once he saw this, he knew right away, he was talking with the real serpent, or dragon, teli.