This question has become a popular one for dedicated nonbelievers to ask, rhetorically of course, because it challenges the Christian conception of God on several fronts simultaneously. Christians believe that God exists, that God is good, that God hears and answers prayers, that God loves us, and that God enjoys healing people.The Gospels include many stories of Jesus healing people of various afflictions, such as blindness, leprosy, and paralysis. In Luke 8:40-56, Jesus even raises a girl from death, and cures a woman with a bleeding problem along the way. Finally, we read that Jesus actually did heal amputees too (an ear in one case, a hand in another).
In modern times, one occasionally hears of someone who prays (or is prayed for) and is cured by God of some affliction such as cancer or back pain. I’ve heard stories like that personally, and there are many others reported online (for example, here and here). It is often asserted by nonbelievers looking to enlarge their number that it is suspicious how God heals internal diseases and pains, but not amputees. I suppose this point has some initial shock value to someone who has heard stories about cancer or back pain but not amputation. However, as it turns out there are reports of amputees being healed too (most famously in the story involving St. Anthony, but also in modern times).
The underlying issue is not some artificial distinction between amputees and those with other ailments, rather it is the general observation that God doesn’t heal people (or otherwise answer prayers) in any setting that will convince everyone beyond a reasonable doubt that He has intervened. We don’t see God work when CNN is rolling tape, or several doctors are standing around a patient, or a scientist is conducting a controlled experiment to be reported in a prestigious journal. We hear about it from ordinary people, and there is always ample room to doubt either their honesty or their interpretation of what happened. In individual cases, perhaps God proves His existence beyond that person’s reasonable doubt, but for the rest of us (myself included), we maintain our faith in God on other grounds (mine are summarized here).
This problem of God being selective about revealing Himself is not new to the scientific age, but is found in the Gospels too. In Luke 23, King Herod challenges Jesus to give him a miracle-on-demand. Jesus could have saved His own skin, won a powerful convert, and spread belief in His divinity far and wide if He had obliged, but He did not. Why might God behave like this? In a separate post, I have offered some thoughts to consider.
Perhaps the other reason why the question about amputees is popular is that it immediately calls to mind the suffering of the amputee, and therefore leads to another one of those uncomfortable questions for believers. Why would a good God allow suffering in the first place? I’ve posted my own thoughts on that one in a separate post as well.