I ship through paypal so I don't know anything about underestimating weight other than to say that I'm guessing it's the post office that is charging them back and not ebay themselves.
I've never seen USPS refund for overpayments (items where you over-estimated the weight). I think their thinking is that as the seller, you're responsible for knowing the weight of your items and/or buying a scale so you can get it right.
Another suggestion I offer is that if the weight of the item is close to the oz. mark, i.e., 3.8 oz.) and you haven't taped the package closed or applied the shipping label, spring for the 5 oz. label (13-cents extra over 4 oz.) because it's likely that the shipping label and will add more than .2 oz and bump your package into the 4+ oz. bracket.
@Catbird9, prices are no longer the same in the 5-8 oz. range.
These are the discounted (ebay/PP) FIRST CLASS prices:
5 oz: $2.79
6 oz: $2.92
7 oz: $3.05
8 oz: $3.18
9 oz: $3.34
10 oz: $3.50
11 oz: $3.66
12 oz: $3.82
13 oz: $4.10
14 oz: $4.38
15 oz: $4.66
16 oz: $4.94
It's possible that you shipped by priority mail and even for a 2 oz. package, you have to pay the price it costs for 1 lb.
Again, I don't think it's ebay who is assessing the charges for overweight or underpaid packages. It's the post office who is charge ebay and ebay is charging the user who made the mistake.