What makes atheists think differently from theists?

They don't take sources at face value...

Give a theist a text, let's say the Bible. Someone let's say a preacher will tell them that it's accurate and correct and they will believe it.

Give the same text to an atheist, they will research it, find out who wrote it, find out when it was written, check it against archeological evidence and other written sources to verify its accuracy, they will then make an opinion based on all available evidence

It is interesting that you use the phrase "what makes atheists" think differently.  No one made atheists think differently.  You and other believers in religious texts were "made" to think the way you do because you were too young to realize that you were being told stuff that no adult would believe if they first heard it at twenty one.  A person who had never hear of the Bible would not believe it if they were told that Noah rowed a boat to Australia to capture kangaroos before his side trip to Montana to collect a pair of grizzly bears.  Being told that kind of crap as a child can forever "make you think differently".   

What makes anyone ignorant of anything? They simply have not yet discovered the truth, though many of them do so every year.

generally speaking they  employ critical thinking skills

to the god proposition  critical thinking is also used

when children  developed the skill and apply it

to the claim of Santa Claus

  test ability , demonstration validity of a claim

  its what the USA court systems  trial lawyers

encourage   when  presenting  a case  and the claims

A working brain........

 Atheists tend to hold a great deal more intellect than the average religious moron is why of course. They also face reality far better than believers tend to do.

Atheists think opposite to Christians because firstly atheists don't believe there is a God and He is THEIR Creator in heaven.

Secondly, atheists have not been born again and before we are born again of God, we are ALL born of the devil, we are ALL born dead in the sins of Adam and we are ALL born into Satan's kingdom of darkness.  When we get born again of God, He delivers us OUT OF Satan's kingdom of darkness and translates us INTO the kingdom of the Son of His love (Colossians 1:13).

 That's why atheists don't have pure or forgiving or comforting thoughts, but thoughts of suicide and death and deception etc., because they follow their father the Devil and He was a MURDERER from the beginning and the father of lies. (John 8:44).

  The Devil is Satan and his only ministry is to STEAL, to KILL and to DESTROY folks, (John 10:10) so it's hardly surprising that his children (atheists who follow him instead of God) hear his whispers and think differently from us Christians who hear God's wonderful voice and follow after righteousness and peace and joy and forgiveness and love of our fellow brethren and those who are different and under-priviledged in the world.

Their lack of skepticism; they'll believe just about anything--except any evidence, no matter how rock solid, for God's existence.  Also, they are very comfortable with intellectual dishonesty.

For example, someone tells them, without any evidence whatsoever to back up the claim, that life came about from a can of Campbell's Primordial Soup left out in the sun a billion years to long, and they believe that one hook line and sinker.

Another example is how atheist SETI observers look to the night sky for any sort of code.  Why?  Codes contain information, and thus are always they result of some sort of intelligence.  But when it comes to the code in our own DNA, they claim that has nothing to do with any intelligence.

Often it’s from expanding their curiosity, knowledge base and possibility. They’re often realists and academically inclined, defying theism. 

We all are products of some combination of nature and nurture, genetics and social upbringing.

Scripture compares believers and unbelievers to sheep and goats.

See why.....

Sheep and goats usually exhibit different behavior. Goats are naturally curious and independent, while sheep tend to be more distant and aloof. Sheep have a stronger flocking instinct and become very agitated if they are separated from the rest of the flock. It is easier to keep sheep inside a fence than goats. Sheep are easier to handle than goats.

Goats will seek shelter more readily than sheep. Neither species likes to get its feet wet and both prefer upland grazing to lowland. In a fight, a ram will back up and charge to butt heads. A goat will rear up on his hind legs and come down forceably to butt heads. During controntation, such fighting behavior favors the ram.

Having a seperate individual brain is a big factor.