Why did Thomas say "My Lord and my God" at John 20:28?
The context of John 20 (indeed, the context and testimony of the entire Bible) does NOT confirm the trinitarian belief that the Messiah is equally God.

Even the TRINTIARIAN NIV Study Bible, Zondervan, 1985, states in a footnote for this Scripture: 

“This whole Gospel is written to show the truth of Jesus’ Messiahship and to present him as the Son OF God, [NOT GOD] so that the readers may believe in him.” 

The context of John 20:24, 25, and 29 shows that Thomas refused to believe that Jesus had been resurrected from the dead. Jesus’ statements before and after Thomas’ exclamation (“my Lord and my God!”) show not only that Jesus wanted Thomas to believe that he had been resurrected to life but that he could not possibly be God.

Jesus’ command to Thomas to literally touch his wounds and actually see his hands proves that he meant, “See, I am the same person you saw die, but now I am alive ... be believing that I have been resurrected to life” (NOT, “see, these wounds prove I am God ... be believing that I am God”).

Notice that the reason given for Thomas to “be believing” is that he can see Jesus’ hands and their wounds. Likewise, after Thomas says “My Lord and my God,” Jesus reaffirms that Thomas now believes (as did the other disciples after seeing - Jn.20:20) that Jesus has been resurrected (NOT that he is God) “because you have seen me” (:29)

John himself has made it manifestly clear that “no one [no human] has ever seen God” - 1 John 4:12, RSV.

If Thomas' statement truly meant that he believed that Jesus was God, surely John would have shown Thomas prostrating himself before “God” and worshiping him (but he doesn’t). So how does John summarize this incident? - “But these were written that you may believe [Believe what? That Jesus is God? Here, then, is where it should have been written if John really believed such a thing:] that Jesus is THE CHRIST, the Son OF God.” - John 20:31, RSV. (Be sure to compare 1 John 5:5.)

This may be, then, one of those places where the idioms of an ancient language are not completely understood by modern translators. 

As the Encyclopaedia Britannica, 14th ed., vol. 13, p. 25, puts it:

"And it is not certain that even the words Thomas addressed to Jesus (Jn. 20:28) meant what they suggest in the English Version." - (Britannica article by Rev. Charles Anderson Scott, M.A., D.D. Dunn Professor of New Testament, Theological College of the Presbyterian Church of England, Cambridge.)

For much more, see:

What did Thomas mean when he said to Jesus, “My Lord and my God”? (Insight-2 pp. 52-72; Watchtower Online Library)
http://wol.jw.org/en/wol/d/r1/lp-e/1200002451#h=26:0-27:1235

Three verses after the account about Thomas, John explained that he wrote so that people “may believe that Jesus is the Christ the Son of God”—not that he is God. (g05 4/22 pp. 8-9; Watchtower Online Library)
http://wol.jw.org/en/wol/d/r1/lp-e/102005283#h=9:0-9:528

Does Thomas’ exclamation at John 20:28 prove that Jesus is truly God? (rs p. 209-p. 220; Watchtower Online Library)
http://wol.jw.org/en/wol/d/r1/lp-e/1101989240#h=22:0-25:919

MY GOD (Examining the Trinity)
http://examiningthetrinity.blogspot.com/2009/10/mygod.html
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