Of course I am excluding those who aren't citizens. Why would they have the same rights as citizens? Citizens of all religions are equal under the law. However, as is in every country, everywhere, there are different rules that apply to different groups. Muslims are not subjected to mandatory military service but Jews are. Muslims can pray openly on the temple mount while Jews can't.
Does having a right of return make a country one mired in apartheid? If so, there's a lot of it going around
en.wikipedia.org
How many Jews sit on the Supreme Court in Iran? Is there apartheid there?
en.wikipedia.org