The 29-year-old Briton, who won gold in the women's road race at the 2008 Beijing Games, said she feared cycling "will never clean itself up."
"I have been robbed by drugs cheats," said the 10-time British champion, who also won the world road race title in 2008, "but I am fortunate. I am here with more in my basket than the 12-year-old dreamed of.
"But for many people out there who do ride clean — people with morals — many of these people have had to leave the sport with nothing after a lifetime of hard work, some going through horrific financial turmoil."
Cooke singled out Armstrong for particular criticism ahead of his interview this week with Oprah Winfrey in which he will address the allegations of doping that led to him being stripped of his seven Tour de France titles.
"When Lance cries on Oprah later this week and she passes him the tissue, spare a thought for all those genuine people who walked away with no rewards — just shattered dreams," Cooke told the BBC. "Each one of them is worth a thousand Lances.
"I have ridden through the time of Lance and all of the dreadful tragedy that the abuses surrounding him have brought to my sport."
Cooke said doping scandals in men's cycling have had a direct impact on the women's sport, including the loss of sponsors.
"With such thin budgets, the losses have a greater relative impact on what survives," she said.
Cooke, whose 13-year career ended in disappointment when she finished 31st in her Olympic title defense at her home games in London, said she had faced temptations to dope but stayed clean throughout her career.
"In my (first) Tour de France, when I was 19, as the race went on, my strength left me," she said. "I was invited into a team camper and asked what 'medicines' I would like to take to help me and was reminded that the team had certain expectations of me during the race and I was not living up to them.
"I said I would do my best until I had to drop out of the race, but I was not taking anything."
Cooke's win at the Beijing Olympics was one of eight gold medals claimed by Britain's cyclists at the 2008 Games.