I make my kids do all sorts of things they don't want to and don't agree with. Clean teeth, shower, wear clothes, turn off the TV, go to bed, be nice to their siblings and friends, stop fighting, not just eat sweets, for example.
I think, as you say, most of us make our kids do all sorts of things that they don't want to do. But we don't try to control what they think and believe, and that's the difference. I think it would be just as wrong to 'indoctrinate' a child that atheism is the only valid path as to push a particular religion. Your kids don't know for themselves that your way is the 'best way to live'. They have been told that by you, and discouraged from examining their own thoughts and beliefs for themselves.
I'm not surprised your 11 year old is confused if the existence of all this is new to her. It's quite a shift to a very protected world view. My five year old is absolutely fine with it because he has always known that different people believe different things about the world and where it comes from, in an age appropriate way. The confusion comes in when my approach is undermined by the school teaching that the Christian god is factual rather than what they, as Christians, believe.
In answer to your direct question, I try to impart to my son the value that all people are of equal value, despite the fact that they may believe different things. I don't think it's truly possible to do that while also taking a hardline 'but this is the only right thing to believe and all those other people are misguided/stupid/godless/can't feel or understand the same level of joy as you/are living inferior lives.' (All things I've had said to me on Mumsnet - the last is the natural flipside of 'knowing' that it's the 'best way to live'.
I don't think 'neutral' or secular is a philosophy in and of itself. It's providing a basis of nothing - the natural state of children - and giving them a platform to discover, question and understand for themselves.