The Yeah! singer dated Thomas for two years before they split in December 2003 amid rumours he had been unfaithful.
Fans believed his record, which features tracks about heartache and betrayal, was about the stars' time together, but Thomas reveals it was actually based on producer Jermaine Dupri's love life at the time.
Despite the relationship ending on bad terms, the Waterfalls hitmaker admits she will always hold a torch for her former partner.
She tells UsWeekly magazine, "We were together when he recorded that album. All of those songs on Confessions, that was about Jermaine Dupri's situation. Usher was just singing it. But people kind of bought into it, it was just the timing of our break-up when the album came out.
"So people assumed that album was about us, but it was not. And Usher and I weren't oil and water. We broke up because I guess it was that time or whatever he was that real love for me.
"In any relationship, even when it came to my relationship with Usher, when it was time to make a move, I had to do that. I don't care how much my heart was hurting, sometimes you're just supposed to be with people for a reason and it's not always a lifetime. Even if you want it to be, it just doesn't work out that way.
"But I'll always love him, forever, because he was my first adult love, a real love. But we're cool, we're really cool. There's no hard feelings, nothing like that. It's all good."