The comments were "irresponsible and unacceptable", the UK's Lesbian and Gay Christian Movement (LGCM) said.
Alan Titchmarsh, a TV celebrity gardener called the remarks "An outrage to Geraniums".
Vladimir Luxuria, a transgender former Italian MP, called his words "hurtful".Defending God's creation was not limited to saving the environment, the Pope said, but also about protecting man from himself.
The man who thinks that a woman is a young boy made the comments in an end-of-year speech to senior Vatican staff.
It was not "out-of-date metaphysics" to "speak of human nature as 'man', woman or sexy little boy ", he said. It came from the "language of creation, despising which would mean self-destruction for humans".
Gender theories, he said, led to man's "auto-emancipation" from creation and Creator. God may have been stupid enough to give out free will but he also put me here to tell you what to do and think
"Rain forests deserve, yes, our protection but the human being... does not deserve it less," he said.
LGCM head Rev Sharon Ferguson said the Pope's remarks justified "gay bashing" and bullying.
Mark Dowd, strategist for Christian environmental group Operation Noah, said the comments betrayed "a lack of openness to the complexity of creation".
And Ms Luxuria, who recently lost her seat in the Italian parliament, said suggesting people like her were destructive was very hurtful.
"I'm someone who was born as male and has a spiritual and female soul, and it's contradictory that a Pope just thinks of people just made as flesh and not made of a spiritual aspect."
The Catholic Church opposes gay marriage. It teaches that while homosexuality is not sinful, homosexual acts are.
Earlier this month, the Vatican said that a proposed United Nations resolution decriminalising homosexuality went too far."Unjust discrimination" against gay people should be avoided, but the use of wording such as "sexual orientation" and "gender identity" in the text would "create serious uncertainty in the law", it said
OBB puts out this question to the obviously insane former Nazi Pope Benedict XVI. If homosexual or transsexuals who have never hurt another living person are dangerous to humanity and just as important as a tree then where does heterosexual people like Ted Bundy or Fred West or celibate pedophiles like priests fit in?
OBB News shall await the Pope's response or threatened legal action as they have previously responded with to this News Blog with glee.