Mary is the Mother of Jesus, not God!” says the evangelical, overreacting to popish claims. It is really a shame that anything that sounds remotely Roman Catholic like “Theotokos” is rejected, the point of the Reformation was not to get rid of everything the Roman church has done but to get rid of its excesses and perversions.
We shouldn’t reject the work done by others just because they aren’t Christian or because they don’t agree with us in other areas. Jonathan Edwards writes
“[We don’t need to] reject all truth which is demonstrated by clear evidence, merely because it was once held by some bad man.”(Words in brackets mine, for context) 
So, because it is popular in Roman Catholic circles, Protestants of both the historical variety (Calvinists, Lutherans, and Anglicans) and non-historical Protestants, which I just prefer to call “evangelicals” for distinction sake, freak out when they hear some Calvinists or Lutherans say “Mary is the Mother of God” as if a bee had landed on them, or perhaps they touched soaked leftover food on a dirty plate in the sink.
There are several misconceptions that occur when you say Mary is Theotokos, the most common objection in my experience is the misunderstanding that when we call her the Mother of God, that we actually believe that she predates God, or that she is the Mother of the Trinity.  This is not the case. The other common misunderstanding is what I quoted above, that Mary is only the mother of Jesus and not God the Son. Such a distinction misunderstands the hypostatic union, for a nature doesn’t have a mother, a person does. Jesus is one person with two natures, not two persons with two natures. The person who claims that Mary is only the Mother of Jesus is unwittingly treating the human nature as if it is a distinct person, which is an error rejected by Chalcedonian Christology. 
In the Scriptures, for example, Luke 1:43, Elizabeth has no hesitation in correctly identifying Mary, we read
“…Why is this granted to me that the mother of my Lord should come to me?” (ESV)
Hmmm, that silly Elizabeth she must have been a papist! Or maybe she understood the ramifications of her statement.Therefore the Lord himself will give you a sign.
Behold, the virgin shall conceive and bear a son, and shall call his name Immanuel. (Isaiah 7:14 ESV)
Immanuel literally means “God with us”(Matthew 1:23) So I have a question, did the divine nature enter the human body after Jesus was out of the womb? Be careful, as such reasoning is dangerous speculation. I hope you’re taken aback at the absurdity of the thought, Through the Holy Spirit (Luke 1:35, Matthew 1:18) The one person of Jesus, consisting of two natures was in the womb of Mary, there is no reason to think otherwise. It was not a mere human nature because a human nature is not a person.
Nestorius rising in Protestant Thought
In my experience as anecdotal as that may be, I am surprised by the number of Protestants who seem to knowingly or not, adopt Nestorian language and conclusions as a sort of overreaction to Roman Catholicism. I reject prayers to Mary, Alphonso Liguori’s statements “refuge for sinners” and “I worship thee” aimed towards Mary , Purgatory, Papal Infallibility etc. However, it is silly to discredit everything a Roman Catholic says because of these errors.
Dr. James White in his book “Mary: Another Redeemer?” states
“Nestorius objected to the use of the word Theotokos….He quite rightly expressed concern that the word could be easily misunderstood……his denial of the propriety of Theotokos led him to insist that Mary was the mother only of the human”element” of Christ, which resulted in a functional separation of the divine from the human in Christ. The basic danger of Nestorius’ position then was that it led to a Jesus who was two persons with no real connection between the divine and human.”
Dr. White goes on to say
“Those who defend the use of the Theotokos did so by insisting that the Messiah was fully human and fully divine from the moment of conception” 
So, to conclude Jesus is one person, with two natures. Natures don’t have mommies, people do. Jesus has one mommy, is one person and has two natures. Are you following the line of reasoning now? God the Son did not originate in or by Mary, but God the Son was in the womb of Mary.
Nestorius will not be victorious.
 Bible.Org “Should we worship Mary?”
 Shameless Popery “Did Luther Want To Start His Own Church?”
 Jonathan Edwards: A Life by George Marsden p. 443
 Wordofhisgrace.org “Was Mary the Mother of God?”
 The Definition of Chalcedon (451 A.D.)
 Visits to the Most Holy Sacrament: And The Blessed Virgin Mary by St. Alphonsus Liguori, p.25
 Mary: Another Redeemer by Dr. James White p. 47