Actually God has been around alot longer then 2000 years, just in different forms. But you know that already. The modern God of the "Book" is a compilation of stories dating back farther then Mesopotamian times. Even the Hebrew religion may have some foundation in Egyption mythology.
Religion is a creation of man to explain the existence of natural occurances like lightning, earthquakes, floods, droughts and volcanoes. As writing became a learned skill, those susperstitions were written down, and through oral storytelling, evolved over hundreds and thousands of years.
Why does religion challenge science so much then? Cuz they know this to be true, and to bury that realization, the science deniers come out in droves. It happened in Galileo's day, and still today.