Prophecy - Son speaking of the Father 

While Psalms 2 can seem confusing at the onset, the best way to handle the Trinitarian doctrine is to try and understand their point of view and put the scripture of consideration into the Trinitarian paradigm. 

Psalms 2

4He who sits in the heavens laughs, The Lord scoffs at them.

5Then He will speak to them in His anger And terrify them in His fury, saying,

6"But as for Me, I have installed My King Upon Zion, My holy mountain."

7   "I will surely tell of the decree of the LORD: He said to Me, 'You are My Son, Today I have begotten You..." 

11 Worship the LORD with reverence And rejoice with trembling.

12 Do homage to the Son, that He not become angry, and you perish [in] the way, For His wrath may soon be kindled. How blessed are   
      all who take refuge in Him!

Take these questions into consideration under the Trinitarian's influence of understanding: 

- We see in Psalms 2:4 that Lord is the same "LORD" speaking in verse 7.  
- If LORD is the proper name of the God of Israel, then is the Son not part of the God of Israel? 
- If Trinitarians believe the Son is a co-eternal member of the Godhead, when did the "LORD" Yhvh beget the Son?
- Matt 28:19 says to "Go therefore and make disciples of all the nations, baptizing them in the name of the Father and 
   the Son and the Holy Spirit," Why then do Trinitarians not baptize according to their own understanding of scripture, 
   being "in the name of Yhvh, Jesus, and the Holy Spirit (who has no other name)"?  

Bottom Line: 
The bottom line is, the LORD is the Lord of us all, meaning that "Yhvh" is our "master/owner/etc". Nearly in all contexts, the lower case word "Lord" is simply a word for authority, even for earthly persons referenced in the Bible, while LORD is a reverent substitution for the actual name of God. Lord can also be used for Jesus, but is not limited to it.

The Pharisees had a problem understanding who Christ was too. They were expecting the messiah to come only once in the splendor spoken of by the Old Testament prophecies concerning the endtimes, not understanding there were going to be two comings of Christ. As a monotheistic faith, the Jews missed the memo that Christ would come in subserviant, human form during His first coming... therefore, since he did not come as they expected, they assumed him to be a false messiah. This is why Jesus was able to trip their understanding in Matt 22:41

"41Now while the Pharisees were gathered together, Jesus asked them a question: 42“What do you think about the Christ, whose son is He?” They said to Him, “The son of David.” 43He said to them, “Then how does David in the Spirit call Him ‘Lord,’ saying,

      44‘THE LORD SAID TO MY LORD,
            “SIT AT MY RIGHT HAND,
            UNTIL I PUT YOUR ENEMIES BENEATH YOUR FEET”’?

45“If David then calls Him ‘Lord,’ how is He his son?” 46No one was able to answer Him a word, nor did anyone dare from that day on to ask Him another question." 

While still in a Lord/master context, they could not understand how the Messiah, prophecied of David in Psalm 110, could have authority over his own grandfather and one of Israel's greatest kings. 

After a confusion of deity references in John 16, he clears it up - 
25"These things I have spoken to you in figurative language; an hour is coming when I will no longer speak to you in figurative language, but will tell you plainly of the Father. 26"In that day you will ask in My name, and I do not say to you that I will request of the Father on your behalf; 27for the Father Himself loves you, because you have loved Me and have believed that I came forth from the Father. 28"I came forth from the Father and have come into the world; I am leaving the world again and going to the Father."

John 14 - Phillip's Confusion 

7“If you had known Me, you would have known My Father also; from now on you know Him, and have seen Him.”

8Philip said to Him, “Lord, show us the Father, and it is enough for us.” 9Jesus said to him, “Have I been so long with you, and yet you have not come to know Me, Philip? He who has seen Me has seen the Father; how can you say, ‘Show us the Father’? 10“Do you not believe that I am in the Father, and the Father is in Me? The words that I say to you I do not speak on My own initiative, but the Father abiding in Me does His works.