Or they're just familiar with a few denominations.
Look at what sincere Christians have claimed is Biblical and you'll find pronouncements that all sorts of things are both sanctioned and forbidden by the Bible:
- Trinitarianism
- slavery
- waging war
- same-sex marriage
- racial segregation
- communism
- child brides
- acceptance of evolution
- voting
- consuming alcohol
- infant baptism
... and on and on.
Chalking all of this up to "angry atheists" seems to me to be just blaming the messenger.
Pick any central tenet of a denomination that is supposedly Biblical and you can find some other denomination that opposes that tenet and cites the Bible to do it.
Christianity have never been a monolithic religion, just one way. Christianity is actually a plurality of richly diverse traditions and ideas which often do conflict with one another. To some, that was and is a problem. Emperor Julian complained that Christians fight among themselves like wild animals. On a more positive note, it means there is freedom, choice. If one church or denomination does not work out for you, there may be another one that does. Different strokes for different folks.