Two things here: 

(1) Based on FPI, BYU's expected win/loss this year is 9-3.  This is not a record that would get them (or anyone for that matter) into the CFP, hence FPI predicts that BYU's chance to be in the playoff is 0%

(2) FPI, also predicts that BYU's chance of going undefeated is 1.1%.  If they were to go undefeated, the probability of making the CFP would go up substantially above 0%.  Not a sure thing, but it is greater than 0%. 

The 0% playoff probability is based on the FPI prediction of BYU's outcome of 9-3 (a 0% probability of CFP).  In fact, the author confirms this when he says that, "even at 12-0 BYU might miss the CFP cut", which, is saying that, "if BYU was undefeated the probability of CFP is not 100%".  This is not news, or even newsworthy.  With the exception of 3-5 teams in college football, the probability of a CFP appearance is not 100% even with a perfect season.  As an example, if Alabama, Oklahoma, Ohio State and Clemson were all undefeated, no other team in the country would even sniff a CFP appearance.  Odds are low that that would happen, but it is why the probability is less than 100% for any team that is undefeated to make the playoff.

Given BYU's start, 9-3 final record and a 1.1% probability of an undefeated season seems like it could be low-balling right now, but if BYU wins another 3 games, those odds are going to start going up pretty quickly.