I'm agnostic, and I believe all people should be treated equally despite sexuality, race, gender etc etc.
However certain religions have problems with gay marriage for many reasons.
Some Christians would point to biblical evidence of God saying only man and women should be together; man cannot be with man (and women with other women). Some use the argument of procreation; sex is a gift from God to create new life, and all sexual acts have to be open to the possibility of creation. Seeing as a gay couple cannot fulfil this in a sexual act, it means they should not engage in it. So some Christians believe plutonic gay couples are acceptable - just not the sex. In terms of marriage, this is seen as union of man and wife, and so some Christians believe the sacred notion of this ceremony is denied if it is not between man and woman. So some support a civil union instead of marriage. Others believe in Jesus' teaching and emphasis of love, and so they believe any relationship and marriage based on love is fine.
Despite their reasonings, even if we do not believe them, it is their belief. I only have a problem with this if it detrimentally affects people, which arguably this does.