Dino Gardiner and Jonathan Lao were released because they wanted to go on trials overseas but Keven Aleman wanted more time to make a decision about his future.
The loss of Aleman is seen as a big one for Toronto because he is a highly-rated midfielder much in the mould of former captain Dwayne De Rosario.
But Toronto's director of player development Paul Mariner, a former Arsenal, Ipswich Town and England striker, says that nobody is bigger than the club and that TFC had no problems in letting the trio go.
"It's a policy decision. What we are doing, we're investing in the academy. It should be an honour to play for Toronto FC, and if people want to ply their trade elsewhere, then that's fine," he told CBCSports.ca.
"We have a lot of experience in our coaching and administrative ranks. We advise players to sign the letter of commitment, but all that does is it protects everybody's interests.
"When you are spending per year in excess of $18,000 on an academy player like we are, then we think it's only right that the player give two years to Toronto FC, and then from there hopefully sign a professional contract.
"Why is Keven Aleman so special? He's not. Every single player at the club is as important to us as the designated player, as the captain, as the super star, as whoever. It doesn't matter. It's the principle of the matter."