In some respect, it's obviously true that science has taken something away from religion. It used to be the case that the primary filter or worldview mediating all perception was religious or belief-oriented in nature. Science has taken a substantial chuck of that real estate. But science has substantial limitations as well; it only talks about things along physical, rather than meta-physical, terms and so is agnostic about the possibility of higher-order meddling. Hindu nationalists for instance have very strong support from many scientists.
The real problem for religion is humanistic attacks against sacred texts and religious practices based on skepticism and comparative analysis. From David Hume to Nietzche, why believe in miracles? You can look at the evolution of every religion as a useful social enterprise which recycles myths, operates in competition with other faiths, and is highly contingent on initial conditions. If every other religion is arbitrary and you don't want to believe in Zeus, then the case for any individual religion takes a hit. You can still be spiritual in general, especially if you get Temporal Lobe Epilepsy.