Is the US government using Shannon as a transit point for those who have been detained by the CIA and are being sent to Guantanamo (or any other prison/detention center)? Almost nobody in the Irish media seems to believe the American government when they answer that question with a 'no'. Yet, the Irish government does accept this.
Why such a big disconnect?
Part of the problem is that the Bush Administration has failed utterly to concern itself with European opinion. It may have been a futile exercise with segments of the media, but that doesn't mean that they should have just abandoned the effort to explain, repeatedly, why such operations as Guantanamo, etc. are crucial in the war against Islamo-fascism.
This failure has allowed the more virulent anti-Americans and the more determined pacifists to monopolize the debate. People like Richard Boyd Barrett, who couldn't even win one of the 28 seats on the Dun Laoghaire County Council at the last local election, are on the radio more often than any spokesman for the US Embassy. Why is that? I'm sure the Palestinian delegation is on the radio more often.
For what it's worth I'm fairly certain that no detainees are passing through Shannon. There's a good practical reason for why this is probably the truth: Shannon is not secure enough. I would imagine that CIA planes passing through Shannon are on any number of possible missions, such as bringing consultants like Joseph Wilson around, but that when they have detainees on board they'd use a military base in Britain or Germany. This is because they'd probably want medical personnel handy and they certainly aren't going to be asking the local GP in Ennis to come down and administer a sedative to a potentially unruly detainee for before his flight departs. A military base would be able to do that much more effectively and quietly.