Pi feels that atheists have faith because they believe in reason, but then go beyond reason to provide further explanation. Further, Pi realizes this because of his "kinship" with Mr. Kumar.
There is an interesting irony that Mr. Kumar, one of Pi's very favorite teachers, is an atheist; however, one of the first words we hear him say is a term full of religiosity. Pi meets Mr. Kumar at the zoo. Reacting to Pi's surprise, Mr. Kumar says, :I come here all the time. One might say it's my temple." Pi is flabbergasted that his mentor doesn't believe in religion calling it "darkness" and explaining more about it:
Why tolerate darkness? Everything is here and clear, if only we look carefully.
Truth be told, Mr. Kumar has been debilitated by polio in his youth. "It wasn't God who saved me--it was medicine." In other words, Mr. Kumar believes in both science and reason. Ho ever, because there are some things that exist but cannot be explained through either science OR reason, the atheist must eventually take that "leap" of faith that Pi talks about here:
Like me, they go as far as the legs of reason will carry them--and then they leap.
For Pi, though, that "leap" was COMBINING religions, not nixing them. For Pi considers it a "terrible disease" that would "kill God" in any person. But what surprises Pi the most is not any of these things.
What I find the most interesting is that it is the connection that Pi feels with Mr. Kumar that convinces Pi that Mr. Kumar actually does have faith.
I felt a kinship with him. It was my first clue that atheists are my brothers and sisters of a different faith, and every word they speak speaks of faith.
Note the pronoun "it" in this quotation. To what does that pronoun refer? It refers to "a kinship." Therefore we could reword the quote to say "[My kinship with Mr. Kumar] was my first clue that atheists are my brothers and sister of a different faith." So, in conclusion, Pi feels connected to Mr. Kumar through science and reason; however, it's Pi's relationship and connection with Mr. Kumar that proves that they BOTH have faith.