The chord progression has three sections. The introduction:
D major | A major | D major | G major
G major | D major | A major | D major | D major
The verses (sometimes halved):
D major | A major | D major | D major
D major | A major | E major | A major
D major | A major | D major | G major | G major
G major | D major | A major | D major | D major
And the bridges and instrumental sections:
A major | A major | G major | D major
A major | A major | G major | A major | A major
One of the first things I noticed about the song after I learned the chords is that it's in 3/4 time. Since the song is about "The Christian life," the three beats to the bar could easily represent the three figures of the Trinity: Father, Son, and Holy Spirit.
Aside from a single E major, the chords are just the tonic (D major), subdominant (G major), and dominant (A major), so there's an-other instance of three. The song is based on musical threes, just as the singer/speaker of the song - who "like[s] the Christian life" - has "built his house on the rock" (Matthew 7:24-27) of the Trinity.
The E major chord contains a G#, which is an accidental in the key of D major. Significantly, the E major (with its accidental) is beneath the lyrics "whole world of" in the line "They say I'm missing a whole world of fun." That whole world of fun contains "things I despise" (that is, sin), and that accidental represents them. The "whole world of fun" is separate from the Christian life in the lyrics, and also in the music, since it's founded on something other than the tonic, subdominant, or dominant.
The first two lines of each verse ("My buddies tell me that I should have waited / They say I'm missing a whole world of fun" and "My buddies shun me since I turned to Jesus / They say I'm missing a whole world of fun") and the first line of the bridge ("I won't lose a friend by heeding God's call") are each four measures long. Since each measure has three beats, each line is a total of twelve beats. Twelve is also an important number in Christianity. For example, there are twelve Tribes of Israel and twelve apostles. Admittedly, this doesn't seem as significant as the other features I've noted, but I thought I'd mention it all the same.
