It is said in the holy Bahir:
"The Torah starts with bet because it has to start with a blessing, bracha."
You can see other times in Jewish scriptures that it begins with a brachach. EXAMPLE: the gemara, and the mishnayos start with tractate brachos, blessings.
But another answer (my personal answer), is:
It is a well known concept that G-d is Aleph. All of G-d's names start with Aleph which makes Aleph the most holy letter in the Aleph-bet. And didn't God come before BeReshet (creation of the heavens and earth)?