The simple answer is that the title comes from the fact that Peter was a fisherman, that he was the first "Pope" so to speak, and that Kiril, the protagonist of The Shoes of the Fisherman, has the metaphorical task of filling the shoes once worn by Peter. 

Here's the detailed explanation: 

The premise of Catholicism is that the foundation of the church lies on the first Vicar of Jesus Christ, Simon Peter, commonly known as St. Peter. 

Simon the fisherman, one of Jesus's twelve apostles, was also the one with the strongest faith. For this reason, Jesus gave Simon the monicker "Cephas" which means "rock."  In Greek, the translation of Cephas would be "petros," which then became anglicized as "Peter." 

Since Peter was the biggest devotee of Jesus of Nazareth, he is also thought of as the rock, or the foundation, of modern Christianity. In Catholic "language" Peter would have been the first Pope because Jesus viewed and ranked him at the head of his ministry. 

Therefore, the title The Shoes of the Fisherman refers to the fact that Russian pope Kiril Pavlovich Lakota has been named Pope, and he is to take the same role as Peter, the fisherman who loved Jesus of Nazareth so much.