Chaucer is not a fan of the Catholic Church as an organization. That is well known. He believed that the local parsons were good people, but that the hierarchy of the church had become irreversibly corrupt.
The pardoners themselves were part of that very problem, so this pardoner is believed by Chaucer to be a greedy hypocrite.
You see, the pardoners were in charge of the sale of pardons, or indulgences, which were basically forgiveness in advance for sins you had not even committed yet. This practice, which is obviously foreign to any Biblical teaching, would eventually spark the mass departure from the church known as "The Protestant Reformation."
So when the pardoner tells the tale of the three travelers that condemns greed and vice, the very things that he demonstrates before and after his tale, it shows that Chaucer is exactly right in portraying him as a greedy, hypocritical person.