Easier said than done. When people become personally invested in their opinions, it's not a simple matter to make them not care. Logic often pales in comparison to emotion when it comes to the motivating factors behind people's approaches to subjects and discussion. Ideally, everyone could accept the opinions of everyone else, but realistically, it's an impossibly steep uphill battle to get frustrated with it. It's best to just let people be offended.
Plus, many people are compelled by their views to attempt to convince others to agree with them. Most religious texts include the assertion that converting non-believers is a means of saving them. Similarly, there's a portion of the atheist community that believes that eradicating religion is the only way to save society. So, they believe that by not arguing, they are doing their belief system a disservice.