1) Does it cost more to ship to Alaska/Hawaii/Puerto Rico?

The answer is a qualified "no". IF you are using USPS and IF you don't live in certain central parts of the US, the cost is no different than shipping to the opposite side of the country. If you live in Pennsylvania it is zone 8 to California and also zone 8 to Alaska, Hawaii, Puerto Rico (and Guam, US Virgin Islands, and other US territories.) The Priority mail cost is the same.

If you are using UPS or FedEx the cost may be substantially higher to ship outside the contiguous US. Those carriers do now offer ground service to Alaska and Hawaii, but it does cost more. USPS is recommended as an alternative for those locations as the rate is much more reasonable.

2) My listing said "US only." My buyer is in Alaska/Hawaii/Puerto Rico!!

Well, those are part of the the US. eBay's shipping details box does not include an option for shipping to the contiguous US only. If your flat rate shipping is for UPS or you have other reasons for limiting where you will ship, you need to clarify that in your item description.

3) The listing said the s/h was for the continental US. I'm in Alaska and that's part of the continent.

"Continental US" has been used for decades by the mail order industries and even UPS to refer to the 48 contiguous states. Your understanding of geography may be superior, but if the seller included a limitation the intent should have been clear. If there is any question or doubt, email before you bid.

4) The listing said the s/h was for the lower 48 states. I'm in Hawaii and that's lower than many other states.

Another gold star for geography but read number 3.

5) My listing said "US only" and my buyer is in Puerto Rico!

Puerto Rico is actually a US commonwealth. Though not a state, it is part of the US. No customs form is required and there are no taxes or other concerns in shipping there. Regular USPS rates apply. There are actually many locations like this. Treat it like any other normal transaction and enjoy your profit!

6) How can I make sure I don't get bidders from Alaska and Hawaii?

First, if you ship USPS, why would you want to? Those members are fellow citizens of the US who just happen to live in locations a little more exotic than yours. Unless you live in one of the few areas that doesn't have any zone 8's in the contiguous states, the cost isn't going to be any higher than that to the opposite coast. If you use the calculator it doesn't matter anyway.

If your items are too large for Priority mail or if your normal carrier is UPS or FedEx, you do need to clarify your shipping policy in your item description. Phrases such as "We ship only to the contiguous 48 states" or "S/h will be $12 within the contiguous US; AK/HI and other locations will be higher" will help you avoid having distraught buyers who post their complaints on P&S, or worse, in your feedback.

7) Why do so many eBay sellers charge a lot more to ship to AK/HI/PR?

Some have legitimate reasons for doing so, primarily using a parcel carrier and basing their flat rate s/h on their costs within the contiguous US. They charge more because it costs them more.

Other sellers are less experienced. They see that some sellers charge more to ship to those locations and assume that it will cost them more. If the seller is using USPS and charging a higher rate you might want to politely email before bidding and, noting that the cost is normally the same as to the other states, ask if the seller could take a look at the s/h fee. (The same applies to auctions that exclude AK/HI/PR entirely.)

If you're a seller, there is absolutely no reason to add a higher handling fee for shipping to those locations. The work is the same as shipping a package anywhere else in the US.