If you have an e-bike with a rear hub-motor (and with the battery pack over the rear tire), you should note that you have considerable unsprung weight on that rear tire. You should try to make sure that you have the tires properly inflated -- on the high end of the maximum PSI the tire can handle.
Try to ask your LBS when you're replacing the tire what type of puncture you're getting. If you are getting pinch flats, then you need to think about inflating your tires to a higher pressure. If that's not possible, you can also explore getting wider tires.
If you're getting road debris punctures, then kevlar belted tires will help. Also, as ow3n notes, having some sealant inside your tube might help although I find that this often just creates a huge mess when you get a flat that is too large for the sealant to contain.