Take them off... leave them off... then put them back on... then leave them on... then take them off again!
Hehe - it's really personal preference.
Mine came stock without anything but after I put 10" rims and 305s on the beast the tires wtuck out wayyy too far, so I found some used from a member here at TS. Now they cover perfectly.
The problem I see with most of the wheel flares on the stock Tundras on the road is that they stick out way too far and make it look really stupid from the rear! Makes it look like you have those skinny little "Cholo" rims/tires on the truck! ACK!
My 2¢ and that's all it's really worth!
Jeff