The feat works fine without multiclassing, if you use more powerful animal companions
Lets say you are a single classed level 7 druid. Your effective druid level with a Dire Wolf and the feat would be1:
7 (your actual druid level)
-6 (adjustment for having a dire wolf)
+3 (adjustment from Natural Bond feat) =
4 (Overall effective druid level)
The feat says that " This bonus can never make your effective druid level exceed your character level.", and it does not. So the feat maybe does not reduce the adjustment for your animal companion, but it modifies the overall resulting effective level, which has the same effect: Your effective level of 4 with the Dire Wolf is not exceeding your character level of 7. You can enjoy the better Dire Wolf, as if you were a level 4 druid.
The limiting clause means you can not to take a plain animal like a dog, which has no negative adjustment to your effective druid level, and be able to enhance it so it works as if you were level 10, instead of level 7. In that case, your effective druid level would be larger than your character level, so that does not work, and you will be capped at level 7.
1 The rules for the Animal Companion on describe the level adjustments for more powerful animal options like this:
A 1st-level druid’s companion is completely typical for its kind except as noted below. As a druid advances in level, the animal’s power increases as shown on the table. (...)
A druid of 4th level or higher may select from alternative lists of animals. Should she select an animal companion from one of these alternative lists, the creature gains abilities as if the character’s druid level were lower than it actually is. Subtract the value indicated in the appropriate list header from the character’s druid level and compare the result with the druid level entry on the table to determine the animal companion’s powers. (If this adjustment would reduce the druid’s effective level to 0 or lower, she can’t have that animal as a companion.)
The last sentence makes it clear that "effective level" means the natural druid level adjusted for the value from the list header (otherwise that adjustment would not reduce the druid's effective level). On that list, as you describe the Dire Wolf is in the column for 7th level or Higher with a modifier of -6.
7th Level or Higher (Level -6)