There are two parts to your question. In Germany, religions were funded by a proportion of taxes. Everyone was a member of the religion into which they were born - unless they formally renounced their membership, becoming either a member of another recognized religion or becoming a dissident. For some places - especially Berlin, the registers of Jews and Dissidents are filed together.
As to the other part of your question, some collections of genealogical records treat births and baptism /christening records as being the same thing. This is due to the biases of the orginizations that have created the collections.
You have to take each record on its merits, and examine it to see what it really is. Personally, I find it offensive when a Beschneidung (circumcision) register is grouped with baptisms and christenings, but I have to get over it and take the records for what they really are. And often, a Beschneidung register is really a birth register - one date column is left blank for the girls.
And lastly, sometimes there really are collections of baptisms/christening of Jews - those are conversions. I hope this helps a little.
Rodney Eisfelder, Melbourne, Australia