Any kind of discrimination is a bad thing, and if it's left unchecked, it can turn into something as ugly as the racial discrimination we saw in this country.
I'm not disagreeing with you that discrimination is a bad thing. But there is not institutionalized ideological discrimination in the same manner that there was institutionalized racial discrimination during the Jim Crow era. There are no laws that force atheists into social subordination.
I'm not saying that discrimination against atheists does not exist. But there is a huge difference between social discrimination and institutionalized segregation. Also, there is a huge difference between racial discrimination and ideological discrimination.
I'm with you here. It's not the same thing. It would be if, say, people were asked for their religious affiliation upon getting on a bus, and they were all honest, and the atheists were sent to the back. Or atheists had hoses turned on them for protesting discriminatory laws. Black people couldn't drink from the white fountain without being questioned, but you couldn't do the same for atheists. We look like everyone else. You can't just pick us out of a crowd.
I will however say that more than social, there is institutional discrimination. The Texas State Constitution among several other states, bans those who don't believe in 'almighty god' from holding public office. Of course this violates equal protection and the establishment clause, but that doesn't always seem to matter I guess. -_-