The 34-year-old recently admitted that he had considered a switch to the Star from the Finn after the 2012 Olympics.
"I'm disappointed," Ainslie said. "I think you will lose a lot of the top sailors from the Olympics."
Britain's Iain Percy and Andrew Simpson won Star gold in Beijing in 2008.
The pair added the world crown to their Olympic title with victory in Rio in January 2010, but will have to change class if they are to return for the 2016 Games.
"I think it's a big shame and I really don't fully understand the decision," added Ainslie.
"There have been massive changes in the last three to five years and real turmoil in the sport, I think it would be really good to get some focus now and move forwards."
The decision to drop the Star was one of a number of controversial revisions, and included axing the Elliott 6m class, which means there will be no keelboat fleets in Brazil.
Since its debut at the 1932 Olympics, the Star has missed just one Games - the 1974 Montreal Olympics. It was provisionally dropped before the 2000 Games in Sydney, before being reinstated - but a reprieve is not expected this time around.
The Star class has been dubbed the "fleet of champions" as many Olympic and world champions often conclude their dingy careers in the boat.
Percy won Olympic gold in the Finn back in Sydney 2000, whilst other successful sailors include two-time Olympic gold medallists Robert Scheidt and Torben Grael, as well as 1996 Finn champion Mateusz Kusznierewicz of Poland.
Isaf's ruling means the Elliott 6m class will appear at only the 2012 Games, before being removed for Rio.
It replaced the Yngling fleet, in which Great Britain's "three blondes in a boat" excelled as Shirley Robertson, Sarah Ayton and Sarah Webb won gold in Athens, before Ayton and Webb were joined by Pippa Wilson to repeat the success in Beijing.
A further suggestion could see the removal of windsurfing, which has been part of the Olympic set-up since 1984, in favour of kitesurfing.
Nick Dempsey, who won a windsurfing bronze medal at the Athens Olympics and was world champion in 2009, says he has serious reservations about the suggestions.
"Kitesurfing is a new sport, it's great, but is it ready for an Olympic Games? I don't think it is," said Dempsey.
"I think it's going to evaluation and hopefully they'll see that it's not ready.
"I hope windsurfing will stay in [the Olympics] and maybe kite-surfing will be in as well come 2020, but they [Isaf] do what they do," Dempsey told BBC Sport.
The Royal Yachting Association (RYA) broadly supported Isaf's decisions.
Racing and performance manager John Derbyshire said the list of events "shows progression within the sport and a clear pathway now, particularly for girls transitioning from the youth classes into Olympic campaigning."
Derbyshire added: "The mood of the meeting clearly showed that the retention of the keelboat events is not the right thing for the future growth and appeal of the sport in Olympic terms right now, and that the events chosen reflect more the mass participation of young sailors within sailing and the RYA supports those views."