I don't want to put words into Matt's mouth, but I can offer a few very quick, brief points of immoral ideas and teachings in the Bible, which I believe he's touched on before:
1) God condones and endorses human slavery in the Bible. There are rules about how you can beat your own slaves (just make sure they don't die within three days, if you beat them), as well as rules about how long you're allowed to keep slaves for (which differ depending on the race of the slave), though there are also rules that can be manipulated which would let you keep a slave forever if he marries. You'll want to look the details up for yourself, but I'm fairly certain that God never once condemns slavery.
2) The idea that killing the son of God somehow provides the eternal promise of redemption for any and all sins, if you just accept him as your person lord and saviour, is pure scapegoating and a disregard for moral responsibility. Responsibility for harm done to others can not be so easily erased by punishing someone else for your wrongdoings. Furthermore, the idea that a raping, murdering neo-nazi can just ask for forgiveness on his deathbed and ascend to Heaven -- whereas an atheist who devotes time to charity and treats others with kindness and respect supposedly is denied a place in Heaven, simply for not believing -- is also extremely immoral and irresponsible.
Also, if there is a Hell, and people go there, then those in Heaven supposedly might have knowledge that those they knew in life are now suffering the worst imaginable suffering for all eternity, and they're expected to be okay with that, and are expected to agree that those people deserve every second of it. Allowing eternal suffering on that scale, no matter what the crimes in life, is immoral in itself. So, too, is eternal reward and bliss for blindly accepting the teachings of the Bible, without rational justification -- "faith" is neither moral, nor a virtue, in the sense that the Bible endorses it.
3) God seems to have complete disregard for human life, and fails to consider innocents caught up in whatever ham-fisted schemes and mass murder plots he's concocted. He floods the whole world, killing absolutely everyone -- and every animal -- except for those on Noah's ark. He sends plagues and diseases to kill the people of Egypt -- including an arbitrary one where every first-born of Egypt would die, just because. He orders Abraham to kill his own son, as proof of his faith (he eventually steps in and stops him, but the fact that Abraham was about to do it means he "passed" the test). He often orders the complete destruction of entire cities and their populations -- sometimes allowing for the saving of virgin girls, for you-know-what purposes.
Here's a cool clip from The Atheist Experience where Jeff and Matt tally up an estimation of the total number of deaths caused by God, throughout the Bible:
Part One: http://www.youtube.com/watch?v=IABptlAhyJw
Part Two: http://www.youtube.com/watch?v=WWHzB6H718w
4) Personally, one of the things I find most repugnant is that people don't just hold these beliefs to themselves -- they try to force these beliefs onto others, especially their own children. Telling a child that we all deserve eternal damnation, and that the only way to redeem ourselves is to disregard reason and evidence-based inquiry and worship a fictional character, is monstrously immoral. Children are impressionable, and will pretty much wind up believing whatever their parents and teachers tell them -- so when you bring them up with religious dogma that cannot be verified, proven, or supported by evidence, you are mentally and emotionally abusing your own children for the benefit of your religion.