There can be a few reasons. First, flat rate shipping does not apply to equipment orders, drop-ship orders, out of stock orders, orders that are international or shipping to Alaska, Hawaii, US territories, APO/FPO or international destinations.
The second major reason orders do not qualify for flat rate shipping is the items are too heavy. Orders with a total weight of 50 lbs or more are not eligible for free shipping.
The problem is that major shipping companies don't calculate their prices on actual physical weight but on something called DIM weight. Dimensional (DIM) weight takes into consideration the amount of space a package occupies in relation to the actual weight of the package.
Anything bigger than 18" is considered a "big" item by them and is given a much heavier DIM weight.
Typical items that have a heavy DIM weight are: 24" x 18" and 36" x 24" Corrugated Plastic Sheets, Wind Sign II, Signicade, Squarecade, Econo Sign, Deluxe Signicade, Floor Racks, Wall Racks, EnduraSTAKES, and some sizes of EnduraMAT.
For more information about DIM weight please visit this article.