I agree with curlytoes's reply
It looks like you never explained importance and meaning of 'Namaste'. Many classes have this issue with using "Om" also. It is ok if you get this response at some place you are representing first time and audience don't know you but in your own class this is pointing your addressing.
Response of student is based on his / her level of maturity and understanding about yoga background.
Remember that Namaste and Om as such have no direct link of yoga (though they are important and have value in it) but having said that I do use three times om chanting at the end and patanjali invocation at the beginning.
I have never faced any issue by any student (of any religion) because in between I keep explaining what is the meaning of what I am chanting. Everybody follows after my lines.
I have never seen this issue in any martial arts when they use Chinese or Japanese terms or lines at the start and end of the class.
You need to educate people about it.
Yoga without flavor of spirituality has no essence and the word yoga (root Sanskrit word "yuj") has spiritual meaning behind it.