All Christians are "in Christ"; therefore they are all one with the Father, and one with each other as well. Notice carefully what Christ says in verses 22-23: "[I pray] that they may be one, just as We are one; I in them and You in Me, that they may be perfected in unity." The basis of that unity is not a denominational affiliation; it is our position in Christ.
Faithful evangelical Protestants believe God is answering that prayer of Christ even now. We enjoy an amazing degree of unity with one another, despite our denominational distinctions. In other words, the kind of spiritual unity Christ prayed for does exist in the true body of Christ worldwide despite denominational barriers. Our Lord's prayer for His church has not gone unanswered.
Christ's true church is not confined to a single congregation, denomination, or earthly organization. The church is composed of all true believers in Christ, regardless of denominational affiliation or membership in any earthly assembly. In the words of the Westminster Confession of Faith, "The catholic or universal church, which is invisible, consists of the whole number of the elect, that have been, are, or shall be gathered into one, under Christ the Head thereof; and is the spouse, the body, the fullness of him that filleth all in all" (25.1). When the Confession speaks of the church as "invisible," it does not mean the church is inconspicuous or utterly hidden from view. It means that its precise boundaries cannot be detected through human perception. There are people who claim to be, and appear to be, part of the body, but they are not. Others, perhaps unknown to us, are true believers and members of the body. The exact boundaries of the true church are not always easy to discern. But nonetheless genuine believers are "all one in Christ Jesus" (Gal. 3:28)—united with Him, and therefore united with one another. "For even as the body is one and yet has many members, and all the members of the body, though they are many, are one body, so also is Christ. For by one Spirit we were all baptized into one body" (1 Cor. 12:12-13).
During His earthly ministry, Christ told the disciples: "I have other sheep, which are not of this fold; I must bring them also, and they will hear My voice; and they will become one flock with one shepherd" (Jn. 10:16). The "one shepherd" is Christ himself, not an earthly vicar. And the "one flock" is also a spiritual reality even now, with believing Jews and Gentiles united in one new body, and the middle wall of partition between Jew and Gentile having been broken down (Eph. 2:14-16). The perfect manifestation of that unity awaits fulfillment in a future time, when "we all attain to the unity of the faith, and of the knowledge of the Son of God, to a mature man, to the measure of the stature which belongs to the fullness of Christ" (Eph. 4:13). In the meantime, to settle for the superficial unity imposed by a monstrous worldwide ecclesiastical hierarchy would be a serious mistake.
The unity Christ prayed for has always existed in the true body of Christ. It is an organic, not an organizational unity. It is a spiritual, not a corporeal unity. And it is not a unity without diversity. (If He had wanted unity with no diversity, He would not have gifted us with different spiritual gifts.) But the kind of unity Christ prays for is a unity in spite of our great diversity.