Many gay Catholic Americans felt shock and disappointment on Wednesday as they awoke to news that Pope Francis had secretly met with a Kentucky county clerk who has refused to issue marriage license to same-sex couples.

The meeting during the pope's six-day US visit on Thursday has sent a shiver through many gay Catholics, who had been hopeful he would push for a Church more inclusive of gay and transgender people.

"It was a kick in the stomach this morning," said Nicholas Coppola, a Catholic New Yorker, referring to the meeting between Kim Davis and the pope at the Vatican Embassy in Washington. "I was the most hopeful with this pope and so this has been the biggest letdown."

Coppola said he feared the meeting would encourage persecution of gay and transgender people, including shunning and violence, in the name of religious conviction.

Rowan County Clerk Kim Davis was briefly jailed in Kentucky for refusing to issue licenses to gay couples after the US Supreme Court ruled in June that same-sex marriage was legal in all 50 states. Davis said that violated her Christian beliefs, and her stance has come to symbolize the sharp division in American public opinion over the issue of same-sex marriage.

Davis' attorney, Mat Staver, said the meeting with Pope Francis was not intended to send a political but rather to encourage Davis to stay committed to her religious convictions.

Gay and transgender advocates, who lobbied the Vatican for in-person talks with the pope during his U.S. visit but were denied, say the meeting with Davis has been deeply insulting.

"This sends a clear message that the Vatican simply doesn't care about millions of devoted LGBT Catholics, who wish to be a part of the Church they love," said Sarah Ellis, president and CEO of GLAAD, a gay and transgender media monitoring group.

The meeting was also puzzling, advocates say, because it apparently contradicted comments made by Francis that have been seen as supporting gay and transgender people.

After he famously replied, "Who am I to judge?" when asked about gay men serving in the clergy during the first year of his papacy, Francis was named person of the year by the Advocate, the largest gay interest magazine in the United States.

More recently, the pope encouraged parents to be more accepting of their gay and lesbian children and met privately with a transgender man at the Vatican.

"Though LGBT and (allied) Catholics have welcomed Pope Francis' affirming remarks, many, including myself, have also remarked that he sometimes talks out of both sides of his mouth," Francis DeBernardo, director of gay and lesbian Catholic advocacy group New Ways Ministry said in a statement.

Pope Francis' comments during his U.S. visit, which were monitored closely by gay advocates for messages about gay and transgender people's future role in the church, were considered vague but not condemning.

Advocates say that while the Davis connection was disappointing, it wouldn't deter their cause.

"We will continue to push to meet with the pope," said Lisbeth Melendez Rivera, head of Latino and Catholic initiatives at Human Rights Campaign, which works for gay, lesbian, bisexual and transgender equality. "We are part and parcel of the church and we're not going anywhere."