What does it mean to "think for yourself" anyway? Either way, people cave in to societal pressures most of the time, and their way of thinking is a reflection of that.
Somehow, "thinking for yourself" means "atheist" nowadays. No, I'd argue that your enviroment shapes your thinking and acceptance more than anything else.
Grow up in a secular home, you'd be non-religious. Grow up in a Christian home, you'd be Christian. Grow up in a Muslim home, you'd be Muslim.
No one really "thinks for themselves" when you think about it -- your thinking is almost always heavily influence by your evironment.
The problem is that people don't form their own opinions. Whether you grow up in a home that follows Religion X, Y, or Z, once you reach a certain age you should be capable of evaluating for yourself whether or not you wish to continue to follow or believe whatever that is.
The Establishment (of Government and of Religion) does not benefit from free thinking, however. If people question what the government or the religion says from an early age, it undermines the government and the religion. As such, both government and religion condition people to not think for themselves. This is a problem, and it is typically perpetuated by religious fundamentalists (atheists included, as the non-religious fundamentalists) and I-Know-Better-Than-You liberals/progressives.
I know plenty of people who grew up in a Catholic home (and several other variants of Christianity) and now do not follow any organized religion. I also know other people who follow their religion blindly without ever questioning them. To the Christians, I say "What about Leviticus?"
But at the end of the day, if someone wants to think the world is 6000 years old and that Noah was a dinosaur wrangler...does that really matter to me? Do I really need to waste my energy telling them they're wrong? That some people want to legislate against such thinking is a far greater problem.