The operating system thread is not thread safe (that statement does not make a lot of sense, but basically, the operating system does not ensure that the intended atomicity of your code is respected).
The problem is that whether two data items are related and therefore need to be synchronized is only really understood by your application.
For example, imagine you are defining a ListOfIntegers class which contains an int array and count of the number of items used in the array. These two data items are related and the way they are updated needs to be co-ordinated in order to ensure that if the object is accessed by two different threads they are always updated in a consistent manner, even if the threads update them simultaneously. Only your application knows how these data items are related. The operating system doesn't know. They are just two pieces of memory as far as it is concerned. That is why you have to implement the thread safety (by using synchronized or carefully arranging how the fields are updated).
The Java "memory model" is pretty close to the hardware model. There is a stack for primitives and objects are allocated on the heap. Synchronization is provided to allow the programmer to lock access to shared data on the heap. In addition, there are rules that the optimizer must follow so that the opimisations don't defeat the synchronisations put in place.