What's the position of main Christian churches about brothers of Jesus? In this article about visit of Jerusalem's Orthodox Patriarch to Moscow, it is said (in Russian) "Первым епископом стал брат Господень по плоти Иаков" "The first bishop [of the Jerusalem Church] became the Lord's brother by blood, Jacob".

I looked in the Wikipedia and it says that Christian churches do not recognize that Jesus had biological brothers: Mary remained virgin throughout her life, and Joseph was not a biological father of Jesus.

Does this difference in opinion indicate that there is a significant point of view in the clergy that in fact Josephus was the real biological father of Jesus or that Mary had sexual relations with Josephus after the birth of Jesus?
Most non-Catholic denominations do not believe in the perpetual virginity of Mary, and fully accept the idea of Jesus having biological half-brothers.  (Only He has God for a Father.)  

From a perspective of Sola Scriptura, there's no support for the idea that Mary remained a virgin through life, and there is Biblical evidence that Jesus had brothers.

*Please do not take the following quote as me endorsing a view that rejects or accepts the perpetual virginity of Mary.  I'm including it to support the paragraph above.

From http://www.gotquestions.org/perpetual-virginity-Mary.html


  So, what does the Bible say about the perpetual virginity of Mary?
  Using the New American Bible, which is a Catholic translation, we can
  see that the perpetual virginity of Mary is not taught in the Bible.
  Matthew 1:25 NAB tells us, "He had no relations with her until she
  bore a son, and he named him Jesus." He, Joseph, did not have sexual
  relations with her, Mary, UNTIL after she bore a son, Jesus." The
  meaning of this Scripture is abundantly clear. Joseph and Mary did not
  have sexual relations until after Jesus was born. Matthew 13:55-56 NAB
  declares, "Is He not the carpenter's son? Is not his mother named Mary
  and his brothers James, Joseph, Simon, and Judas? Are not His sisters
  all with us?" Catholics claim, correctly, that the Greek terms for
  "brothers" and "sisters" in these verses could also refer to male and
  female relatives, not necessarily literal brothers and sisters.
  However, the intended meaning is clear, they thought Jesus to be
  Joseph's son, the son of Mary, and the brother of James, Joseph,
  Simon, and Judas, and the brother of the unnamed and unnumbered
  sisters. Father, mother, brother, sister. It is straining the meaning
  of the text to interpret “brothers” and “sisters” as "cousins" or
  "relatives" with the mentioning of Jesus' mother and father.


However, there are Protestant denominations that still accept the doctrine of the Perpetual Virginity of Mary.

The view on whether Jesus had biological brothers is, therefore, varied, and the view hinges on whether or not you accept that doctrine.

For more on Protestant views on the doctrine of perpetual virginity, see What do Protestants say was the source for the doctrine of the perpetual virginity of Mary?