There is a way to do that, provided that the flat rate for items that charge shipping will be consistent across all items.
For this to work you would set the weight of all free shipping items to zero, and set the weight of items which charge shipping to 1. Then create rules with the following settings, ignoring any not mentioned:
For orders which do not have any shipping costs:
Shipping Rate Calculator: Flat
Shipping Amount: 0.00
Country: US
Min Weight: 0
Max Weight: 0.9
For all other orders:
Shipping Rate Calculator: Flat
Shipping Amount: 2.49
Country: US
Min Weight: 1
Max Weight: 0 (this means no upper limit)
If this won't work, please let us know your complete shipping requirements so that we can give you more specific instructions.