Thomas, 50, defended the disgraced former Tour de France champion as the 43-year-old Texan joined the ex-England footballer on the tour route.
Armstrong, stripped of his seven titles for drug abuse, is riding Thomas' One Day Ahead fundraising event.
Thomas, like Armstrong a cancer survivor, said: "What is wrong with him doing good in the cancer community?"
Armstrong has teamed up with the former Crystal Palace midfielder to ride two stages ahead of the main tour to raise £1m for Cure Leukaemia, starting with today's stage 13 from Muret to Rodez.
Thomas is tackling the 3,360-kilometre route of this year's race to celebrate the 10th anniversary of entering remission and riding the 2005 tour course.
He told BBC Sport: "It was time to give him a chance.
"I was given three months to live in 2003, I read Lance Armstrong's book, and it was his focus of fighting cancer that inspired not just me, but millions of others.
"I knew the idea of getting him involved would divide opinion.
"But looking at the bigger picture, we've got world awareness of what we're doing to help generate more money for the professors and doctors that we're supporting.
"He has apologised, but some people won't accept the apology."
Brian Cookson, president of the sport's governing body the UCI, said Armstrong was not welcome. But Tour de France leader Chris Froome says he understands the charity element, having lost his mother to a cancer-related illness.
Thomas added: "Lance is a cancer survivor who has raised hundreds of millions of dollars to help research. I thought it was time to give him a chance.
"He's not going to race again, but from what I've seen he's more upset at not being able to get back into the cancer community.
"He's given us profile obviously, but we hope on the back of that he goes back to helping bigger cancer communities and doing good again."
Armstrong feels that he may never be accepted back by the cycling world.
He told BBC Sport: "I think I've got a lot to give in the fight against cancer, but that's not really for me to decide.
"My credentials in that world are pretty legitimate and I stay committed to it. But I don't know if cycling will ever accept me back."
Geoff Thomas says Lance Armstrong deserves another chance to contribute to the fight against cancer.