I believe these verses mean precisely what they appear to mean, and that is why many Protestants (but certainly not all) have shyed away from them for fear that they seem too 'Catholic.'
I believe they do mean that authority is being given to the disciples, authority that has the full weight and bearing that it has eternal effects.
Disbelieving in Paul, and ignoring his Scriptural commands, is detrimental to your health -- both physically and spiritually. Paul, I believe, had the authority and power from God, promised by Christ, to bind and loose on earth. These disciples gave us the words of God, the new commandments and instructions, warnings and rebukings. These rebukes, should we fail to heed them, are binding on us even unto heaven; we cannot escape them.
Because it sounds a little too much like other denominations that some Protestants prefer not to see in the Scriptures, this verse has often been stripped of its meaning. I believe it is giving great power and authority to these disciples. I also believe that the church was indeed in a sense 'built' on Peter, and not 'Peter's confession that we can all confess, that Jesus is Christ as Lord and Savior.
I hope this helps! Just letting Scripture speak is a powerful and life-changing thing!