Ah, educating the young. A task made both easier and harder in the Age of (Mis)Information.
A book that I grew up with is Life Story
, by Virginia Lee Burton. It's a bit dated (was published in the early '50s), but is decidedly secular in its approach. Beautifully illustrated (Burton is a painter), it does a good job of showing the immensity of time and the wonder of discovering knowledge.
Another author is Holling Clancy Holling, in particular his books Minn of the Mississippi
. Both of those are more about natural history than anything else, but also touch on evolution, geology, biology and history; showing the connections between different branches of science.
You might try the "grains of sand on a beach" being a year each, or "stars in the sky" on a clear night as a year each.