Being filled with the Holy Spirit meant to be filled with the words of the Holy Spirit, to speak the truth / words of the Holy Spirit. Look at the first action the people began to do in Acts 2:4... "began to speak".
Philip opened his mouth (Acts 8:35) and began to teach the eunuch. Those that had been filled with the Holy Spirit were prophets, some teachers, some interpreters (understanding foreign languages), some apostles (1 Cor. 12:28-29). All of these were speaking the words of the Holy Spirit as they were moved to do so.
"because no prophecy ever came by the impulse of man, but men moved by the Holy Spirit spoke from God." (2 Pet. 1:21, RSV)
This verse makes it clear that being filled with the Holy Spirit was an occurrence as they were moved by God to speak. It indicates as the Holy Spirit moved them, so being filled with the Holy Spirit was not a permanent condition.
"Now these be the last words of David. David the son of Jesse said, and the man who was raised up on high, the anointed of the God of Jacob, and the sweet psalmist of Israel, said, 2 The Spirit of the Lord spake by me, and his word was in my tongue." (2 Sam. 23:1-2, KJV)
It happened to the prophets of the Old Testament, too. It does not mean that wisdom was always imparted, nor does it mean that the prophet or Apostle was error free, nor does it mean that the prophet or disciple always understood what the Spirit gave him to say. Paul had to reprove Peter publicly (Gal. 2:11), and both Paul and Peter had the Holy Spirit given to them.
and the Comforter, the Holy Spirit, whom the Father will send in my name, he will teach you all things, and remind you of all things that I said to you. (John 14:26, YLT)
The Holy Spirit was going to comfort Jesus' disciples by reminding them of all the things that Jesus had said. He was going to teach them the things they needed to know, to understand what Jesus had told them before.
What did Elizabeth do when Mary came to see her?
"And it came to pass, when Elisabeth heard the salutation of Mary, the babe did leap in her womb; and Elisabeth was filled with the Holy Spirit, 42 and spake out with a loud voice, and said, `Blessed [art] thou among women, and blessed [is] the fruit of thy womb;" (Luke 1:41, YLT)
And, John's father Zacharias also was filled with the Holy Spirit.
"And Zacharias his father was filled with the Holy Spirit, and did prophesy, saying," (Luke 1:67, YLT)**
Peter and John were taken before the Sanhedrin (counsel) and spoke the words given to them by the Holy Spirit.
"Then Peter, having been filled with the Holy Spirit, said unto them: `Rulers of the people, and elders of Israel," (Acts 4:8. YLT)
When Peter and John told the others what had happened,
"And they having prayed, the place was shaken in which they were gathered together, and they were all filled with the Holy Spirit, and were speaking the word of God with freedom," (Acts 4:31, YLT)
Being filled with the Holy Spirit means to be filled with the truth of God's word, the word of the Holy Spirit so that they would speak the truth of God's word to the people.
John's role was prophesied from old (Mal. 3:1) to be clearing the path for the promised Messiah. He was filled with the Holy Spirit in order to do that job, but John did not live to see the kingdom established, nor to take part in the birth of the church on the day of Pentecost. The context of Matt. 11 was speaking of the prophets from the ages before from the Old Testament, under the old Mosaic covenant.
"For all the prophets and the law prophesied until John." (Matt. 11:13, KJV)
John was the last prophet under the old covenant. Once Jesus came preaching the truth that the kingdom was at hand, the gospel of Christ took over, and the old covenant began to wax and perish (Heb. 8:13). Jesus' disciples and Apostles were prophets under the new covenant of the His gospel, His everlasting kingdom.
Jesus did not mean that John was in any way unimportant, or of no consequence; only that a better covenant was taking over.