"Our concern is her long-term health, number one, and her long-term development as a player," McEnroe told the Wall Street Journal. "We have one goal in mind: For her to be playing in [Arthur Ashe Stadium] in the main draw and competing for major titles when it's time. That's how we make every decision, based on that."
Townsend's mother put together the money herself and paid for her daughter to make the trip to the tournament.
"I just felt like with what Taylor had been doing throughout to the summer, her results, and the fact that she was number one in the world, why not?" Townsend said.
After competing in the 2012 Wimbledon Championship in July, Townsend was only allowed to compete under USTA sponsorship in one more tournament in Vancouver.
Townsend reached the semi-finals at the U.S. Open on Friday, but lost 6-4 6-4 in a tough match against Anett Kontaveit of Estonia.
She was disappointed and upset that she didn't play her best, but her mother said she was ultimately just fine.
"She was OK. She said that she didn't play as well as she wanted to play," Townsend said. "But I was proud of her."
ABC News' Tanya Rivero contributed to this report.