As with any pre-pay rate, the answer is "it depends".
Car rentals are one of the last areas of travel where you can cancel a booking at the last moment or even "no-show" without paying any penalty. Try that with a flight, a hotel, a tour, etc and in almost all cases you're going to be out at least a percentage, if not the entire cost.
Rental car pre-pay normally means that if you want to cancel or even change your booking, then you're going to have to pay at least a fee. So in effect, you're giving up some flexibility and taking some (financial) risk in order to get an (apparent) saving.
So what it really comes down to is how much is the savings? Normally pre-pay savings are only 10-15%, which is frequently no more than you can get using other promotion codes with the rental company, or affiliate discounts like AAA (car club) membership discounts that are offered by many rental companies.
For such as small (if any) discount, the answer if simple - no, Pre-pay rates are NOT a good idea and should be avoided at all costs.
However, there are exceptions. For example, consider this quote from Hertz :
In this case pre-paying drops the price from 68 British Pounds to 39 Pound - a saving of around 43%! Unless you think it's likely that you'd be likely to cancel/no-show for the reservation, then obviously the pre-pay rate would be a great deal!