Columnist Frank Rich raises the issue of whether The New York Times is anti-Catholic by his excoriating column attacking  Bill Donohue's Catholic League complaints about a Smithsonian exhibition last Sunday.
On the one hand several of The Times columnists are Catholics.  Nicholas Kristof's father wrote editorials for the Diocese of Portland's newspaper.  On the other we have the sports department columnists Carl Rhoden and Harvey Araton who aggressively attacked Notre Dame University, Rhoden over the firing of black coach Tyrone Willingham.

When Willingham was fired by Washington, The Times didn't carry the story. Araton and others in the sports department savaged two Duke lacrosse players and their Catholic high schools over an an alleged rape.   Turned out the rape never happened. 
Nicholas Kristof, who often chides others for ignoring scientific evidence, habitually blames the Catholic Church for AIDS in Africa because it condemned the use of condoms.   There is no scientific evidence of a correlation between Catholicism and AIDS and it's dubious that anyone who ignores the Catholic Church's proscription on sex outside marriage is concerned about the church's position on condoms.
The Times perennially features the McMansion ethnic slur,  the Irish as perpetrators of the New York City draft riots, and Simon Winchester the anti-Catholic who eventually admitted writing stories for the Guardian that covered up British army killings of civilians in Northern Ireland.
Connecting the draft riots to New York's Irish is especially problematic.   Although the Weinstein brothers' Gangs of New York movie about the riots features the Irish in the Five Points neighborhood, near where my great-grandfather lived,  most of the violence occurred along the 20th-30th street axis uptown, as Pete Hamill pointed out in a Daily News column.  Indeed the lynching of Abraham Franklin recounted in Bob Herbert's egregious column about the riots occurred virtually on the doorstep of Mount Sinai Hospital's original location.   Although Herbert identifies a teenager who mutilated Franklin's body as Irish, the person charged with the lynching was not mentioned: he was neither Irish nor Catholic.  Neither were the commercial interests who incited the rioting, notably the leader of the Democratic party at the time, August Belmont.
Mr. Herbert egregiously accused poor immigrants of refusing to fight to free poor blacks.   MIA, as far as The Times is concerned, is the fact that most of New York City, including the Irish, didn't riot in July 1863.   MIA the Great Militia Mobilization of June 1863 that sent 15,000 men to the aid of Pennsylvania when the Confederates invaded, but stripped New York City of its self-defense force leaving it to the mercy of malcontents.  MIA New York City's 200 Civil War Medals of Honor.  MIA the 200,000 soldiers from New York City including Brooklyn who fought for the Union.  MIA their 20,000 dead.  MIA New York City's Irish Brigade and its suicidal assault on the stonewall at Fredericksburg on December 13, 1862, on the eve of Emancipation.  MIA the Excelsior brigade at Gettysburg.  MIA New York City's 69th Fighting Irish regiment, which fought in almost all the major battles in the East from Bull Run to Appomattox, losing more KIA than any other Union army infantry regiment, some of its members even accompanying Sherman on his march to the sea.
Finally, to illustrate universality of this problem, The Times science department refuses to note that the Large Binocular Telescope (LBT) is by far the largest single mount optical telescope in the world and has produced observations clearer than the Hubble Space Telescope.  Given The Times position that religion, and particularly the Catholic Church, is an antagonist of science, the Gregorian calendar notwithstanding, the science department is loathe to acknowledge that LBT sits next door to the Vatican Observatory in Arizona and the Vatican Advanced Technology Telescope, which was the prototype for manufacturing LBT's gigantic mirrors.
What we have here is what the British call Whig history, a world saved by stouthearted Cromwells and Marlboroughs from the Irish, Spain, benighted Kings, and the Catholic Church.  Wonderful fairy tales for those who like cultivated prejudice and to read that someone else is the problem.