The Stop further rules processing flag allows you to make relationships between different rules. Your store will execute the shopping cart rules in order of priority. IF the system reaches a rule with the Stop Further Rules Processing flag it will stop going through any lower priority rules. This allows you to make some rules exclusive.
For example, you can make a discount coupon with priority value of "10" and a daily discount of priority "5". The coupon gives you $10-off. If the coupon is not used, the cart gives $5 off. If the coupon is used, now the cart is giving $15-off.
If you want to disable the regular discount when the coupon is used you can set the coupon to have the "Stop Further Rule Processing" option to YES. This will keep the $5-off rule when the customer is not using the coupon. If the customer does uses the coupon code, it will disable the $5-off rule and only do the coupon action. The result is a $10-off discount instead of the undesired combined $15-off discount.