Jones admits he was surprised England chose not to include the United striker in their squad.
The academy coach told Ladbrokes: "Listen, the type of players that England have got to pick from these days... it's an absolutely incredible pool of talent, and so you're always going to be left with a couple of big players missing out. Obviously Marcus Rashford is the big call.
"Jordan Henderson hasn't played as much football this season, you know, he went out to Saudi Arabia and then obviously moved to Ajax. He's a massive character in and around that dressing room and his experience will be missed, but Rashford is the one I would identify as the biggest decision."
He added: "It's a tough call, and I'm not saying it's the right or wrong call. I always think Marcus - even if he's not had the season he'd have liked - has the ability to do something special. I know him as a person, and as a player, and I think he could have certainly offered something, especially in games where we're struggling to break teams down.
"You know, he's got that little bit of brilliance - that little bit of magic where he can just take it out of his feet, whip one in the top bin and win you the game. But, again, there are so many talented players to choose from - so there's always going to be someone who misses out, and unfortunately it's him this year.
"I know he'll be so determined to make that right, and get back into the international set-up as soon as possible. Marcus has had a lot of criticism in recent years, but people don't really know him as a person. It's easy to judge people from the outside. It's easy to call people out when you're not involved, and you've not been in and around that environment. It's very easy to judge people.
"Marcus is incredibly talented. He's one of the best players I've ever played with. He's got a strong mentality, he's level-headed and he has a good support network around him. I'm sure he'll come back firing next season... I'm sure he'll have a good pre-season.
"He's the type of guy who'll go away this summer and work on himself, making sure he's in the best possible condition to start next season. He'll know there is pressure on him next season, but I have no doubt that he'll have a much better season than perhaps the one he's just had."