I understand that Psalm 2:7 is talking about Jesus but what do the words
“Today I have begotten you” mean? Is he referring to physical birth? If
not what is it talking about?

I would say that the most obvious place to look for an answer
is in John 1:14. “We have seen his glory, the glory of the one and only
(also translated the only begotten) son. The son of God was not
“begotten” by God in the sense of being created, as God cannot create
himself. Jesus Christ, being deity, was not created. As it says in John
1:1, “he was with God in the beginning.” John 1:14 answers your question
in very plain terms: The Word became flesh and lived for a while among
us.” When the Bible describes Jesus Christ as “begotten” (a word not
appearing in more modern translations) it is referring to the
incarnation. The word “incarnation” is a fancy theological word which
refers to God the Son coming and living in a physical human body. I am
convinced that Psalms 2:7 is a reference and prophecy of the physical
birth of Jesus, the Son of God.

John Oakes