This article argues that the Bible refers to God using male terms because this serves as an analogy to explain the relationship between the Father and the Son. The use of the phrase "the begotten Son" has a non-physical aspect, and this non-physical aspect is emphasized by the use of male terminology.
What is the meaning of calling Jesus the only Son of God? Calling Jesus the only begotten Son of God makes Jesus unique, because He is not the same as the sons of God. Confessing Him to be the Son is not a denial of His divine nature, but rather a confession of His relationship with the Father. This doctrine is described in the Nicene Creed.