Is Odin Thor's father?
Before you automatically downvote this question, I highly suggest reading this article: Thor vs. Odin.
The article background covers the relationship of Thor and Odin, and reveals that things are not as straight forward as is commonly believed:
The name of one king there was Munon or Mennon. He was married to the daughter of the high king Priam; she was called Troan. They had a son, called Tror; we call him Thor… [he meets Sif, his wife, and]… Their son was Loridi, who took after his father… [for 16 more generations, until] … He had a son whose name was Woden, it is him that we call Odin.
SOURCE: Prose Edda, Prologue (Faulkes)
What's the deal?
Also, why might have Snorri presented this alternate version in the prologue? (He sticks to the conventional version in the main text, so it's not unreasonable to assume some intent.)
As you say Snorri Sturluson writes this cited text in the prologue to his Prose Edda, one of our chief sources of Norse mythology. The old Scandinavian worshipers did not have a written language comparable to that of Latin of the Roman church. As such we have next to nothing about the Norse myths written by Scandinavians who were actively telling these myths and believing in these Norse gods, such as Odin and Thor. Instead we must rely on sources written after the conversion of the Scandinavian homelands and colonies to Christianity.
Snorri wrote his Prose Edda some 200 years after Iceland converted to Christianity, at this point the worship of the old gods had faded. But some of the myths were still known either from scaldic poetry or eddic poems of which he cites throughout his edda, many of them are preserved in the poetic edda. Snorri wrote his prose edda to serve as a handbook to these myths, before they were forgotten. But as a Christian in a Christian society this is not always seen as a good thing, and could get him in trouble. So instead Snorri wrote in his prologue that the gods of old were in reality great men and kings that went north and settled in Scandinavia, here their rule were so beneficial to the Scandinavians that over time they became gods in the mind of the Scandinavian descendants. This approach to gods is called Euhemerism, when you say gods are in reality misremembered heroes and legendary men/women.
Thereby Snorri has made it clear to his audience that this his Prose Edda is not to be taken as a pagan text that could land him in trouble, and thus he is free to present the actual myths and gods in his main text.
So to answer your question: Disregard the prologue and look at the main text. Odin is Thors father.