It has become almost reflexive for secular folks and rebellious Christians I encounter to state as fact, "well, how can any religion be true when religious wars and oppression have been the source of so much of the evil in history?"
My response is always triple.
First - yes, 'the Church' and individual Christians have much to apologize and ask forgiveness for. In fact I once began a sermon asking the forgiveness, on behalf of me as a representative of the worldwide church, of the women present for some of the specific ways in which the Christian church had historically been party to the oppression of their gender. This moment of honesty about the past became a point of release for a feminist faith-inquirer who was there that day. Another example I often give - our church land was once part of a cotton plantation worked by slaves. We held a purification ceremony for our land some years ago, at which the leadership of a local African-American church (which was founded by some of those slaves after emancipation) graciously received our historical confession and request for forgiveness on behalf of white American Christians who had indulged in this origianl American sin. It was a powerful prayer event.
Second - as a student of history, I take on the most common statement such folks use as a means of keeping the Christian faith at arms length, that 'wars in the name of Christianity...' etc. My honest conclusion is that where wars have been fought in the name of Christianity, or any other religion, these are almost always examples of leaders and populations using religion as a pretext, a rationale, to indulge one of our most base sinful tendencies - to attack, demonize, and even destroy 'the other' who is 'not like us.' Most commonly, such conflicts are nakedly ethnic in nature, and a true historian can see how religion was applied as a powerful veneer to cover over the nasty truth that one tribe has chose to exert their 'will to power' in a nakedly social dawinistic manner to subjugate or wipe out another tribe. It is a heinous sin for Christian leaders and people to subject the name and the church of Jesus to defamation in such a violent and cynical way. This reflects on the ongoing sinfulness of people and groupings of people, not on Jesus.
Third - I recount some of the ways that quite the opposite is true - the movement of Jesus, the church, has been and continues to be an ongoing primary force for much that we would name as 'good' in this world. In the words of NT Wright (in his introduction to John Ortberg's new book: "Who Is This Man?"):
"(O)ne of the Big Lies of Our Time (is) the assertion that Christianity has been part of the problem rather than the source of the solution. Most people today don't realize that things we now take for granted, like education and health care, were reserved for the rich elite in the ancient world until the Christians insisted on providing them for everyone within reach. Many imagine that Christianity was bad for women, whereas early Christianity provided the biggest transformation of attitudes to women the world has ever seen. (In this new book Ortberg) tracks these and much, much more back to Jesus himself. (We) know very well that the church often gets it badly wrong. But the impact of Jesus on the whole world, even when his followers have been muddled or misguided, towers breathtakingly over all human achievements. This book provides enormous encouragement both to celebrate what Jesus' followers have done in the past and to stimulate a fresh vision of our mission in the future. And, above all, to be amazed and awed once more at Jesus himself, who lived, died, and rose to launch such a transformative vision."
I hope these thoughts are helpful to you, if you wrestle with this question and/or have friends who do. Ortberg's book is the best place I know of to keep at this question doggedly if its a particular stumbling block in your or a friend's life.