Yeah, I think that's how the method is intended to work. The sum of all the percentages should give an estimate of how many active players will reach the goal. When Bill James developed the formula, he tested it by looking at how it would have worked in the past.
In the 1990 Baseball Book, he wrote about the 3,000 hit candidates of the era. I'll quote it here:
"On the list of current players with a chance to get 3,000 hits in their careers, Molitor's name is the big surprise. The top ten are Robin Yount (94%), George Brett (58%), Eddie Murray (46%), Kirby Puckett (44%), Wade Boggs (39%), Don Mattingly (33%), Paul Molitor (33%), Tony Gwynn (32%), Carney Lansford (29%), and Steve Sax (28%). It is likely that about seven active players will get to the 3,000 hit standard. Other players with a ten percent chance or better include Cal Ripken, Mike Greenwell, Dwight Evans, Rickey Henderson, Julio Franco, Harold Baines, Ruben Sierra, George Bell, Tony Fernandez, Ryne Sandberg, Andre Dawson, Tim Raines, and Will Clark."
In retrospect, there were actually 11 active players who made it to 3,000: Molitor, Murray, Ripken, Brett, Yount, Gwynn, Boggs, Henderson, Palmeiro, Biggio, and Winfield. The last three of those names didn't make James' list of likely candidates. At the time, Palmeiro was 24 and had a total of 411 hits; Favorite Toy estimated his chance at 4%. Biggio was 23 with 140 career hits; Favorite Toy didn't see any chance of him reaching 3,000. Winfield was at the opposite end of the spectrum: 37 years old, with 2,421 career hits. Favorite Toy didn't see Winfield as a good candidate because he'd just missed the entire 1988 season with an injury, which dropped his established hit level all the way down to 86.
It's interesting to watch a player's chances wax and wane.