The church's spokesman, Peter Kearney, spoke out in an interview published in The Herald today.
Mr Kearney revealed he received 1000 emails attacking him from followers of Richard Dawkins after the atheist posted on his blog that Mr Kearney was "a nasty little weasel".
Mr Kearney's crime in Mr Dawkins's eyes had been urging the SFA to sack its head of referee development, Hugh Dallas, because he forwarded an offensive email cartoon of Pope Benedict before his visit to Scotland.
Mr Kearney said: "Scotland remains a hostile environment for Catholics to live in. Priests have bricks thrown through their bedroom windows.
"The number of crimes motivated by anti-Catholic intolerance has gone up every year since the 2003 Criminal Justice Act was created. Things are not getting better."
He also discussed how he dealt with the controversy surrounding his disgraced former boss Cardinal Keith O'Brien, who admitted inappropriate sexual conduct before going into exile.
He said: "I'd never handled anything like that before. The sheer scale of it was bigger than anything I'd ever dealt with, including the Pope's visit to Scotland in 2010.
"I'd already made arrangements for broadcast journalists to interview Cardinal O'Brien in Rome after the conclave, so it was easy for them to switch swiftly to this new development.
"I got 100 calls that Saturday night alone. They all wanted to know: 'Is it true about the allegations of inappropriate sexual behaviour? Is he going to the conclave?'"
Glasgow University graduate Mr Kearney said he knew nothing of the Cardinal's misconduct, saying: "It was really, really difficult to find myself in the position of asking those sorts of questions to someone I'd worked with very closely over the years."
The crisis has made the spokesman's position stronger. He said: "My voice is heard, my advice is taken, and there is respect given [from Church colleagues]."