The conflict between Roman Catholicism and the legalization of gay marriage exists on many levels. It's more than merely the opposition of clergy to a law or system they find immoral: it is instead a fundamental conflict between basic principles of Catholic theology and basic principles of the modern, liberal society.
One of the problems is the fact that Catholics have been experiencing great difficulty in getting other Americans to even understand their perspective on gay marriage, much less actually go along with it. More and more people are adopting tolerant attitudes towards homosexuality and Catholics can't get people to understand that there is something intrinsically wrong with it all. This is the first conflict: Catholic teaching proceeds from an understanding of "natural law" which for them serves as the foundation for all correct morality but which most of the rest of society has long since abandoned.
Unfortunately, arguments "from nature" don't carry a great deal of weight these days. The mere fact that something is common in nature does not necessarily provide a reason why civil laws must be set up in a certain way. Moreover, arguments from nature have a habit of backfiring - for example, today we know that homosexual mating happens quite a lot in the animal world. If we are to use that as our model, then we could conclude that a certain percentage of homosexual couples is entirely natural and not at all "disordered" (as Catholic teaching claims).
A second conflict involves the relationship between religious leaders and political leaders. Pope John Paul II has specifically argued that gays should not be allowed to enter into any kind of official union that might be considered "marriage," and the Vatican has launched a global campaign to oppose the legalization of any sort of gay marriage. The Vatican has, in fact, instructed Catholic officials that they are required to oppose any such legislation and critics feel that this represents an inappropriate intrusion into political affairs.
Because this involves civil laws that apply to everyone in society and not simply doctrinal instructions that only affect Catholics, a great deal of public discussion and debate has ensued. Does the Catholic Church have any justification for insisting that gay marriage is necessarily invalid, no matter what the laws might say? Is the Vatican inappropriately interfering with civil law and civil society by trying to impose a narrow and religious understanding of marriage on everyone?
Many critics would answer "yes" to the second question above, and herein lies a third level of the conflict: are critics simply engaging in Catholic-bashing and anti-Catholic bigotry when they complain about the Vatican's actions? Defenders of Catholic tradition are emphatic in answering "yes" to this, arguing either that there wouldn't be so much debate if anyone other than the Catholic Church were involved, or that if there were, then the vehemence of the complaints wouldn't be as strong.
These are all interesting and difficult questions. Critics of the Catholic Church are quick to accuse Catholic leaders of returning to the "bad old days" when church leaders tried to rule society and impose their ideas of religion on everyone. Defenders of the Catholic Church are equally quick to accuse critics of returning to their own "bad old days" when Catholics were treated like second-class citizens on the presumption that they owed more loyalty to Rome than to their own nation. Is there any truth in any of these claims?