The eBay fee increases affect anybody who sells on eBay, with a store or not - they didn't add any NEW fees or anything, but almost all of the features were increased (, at least a little. They do it every year, but usually not this much!
I have a "featured store" which is the "second tier" one which is already $50 a month, and it didn't increase (only the lowest one increased from $10 to $16). With eBay stores (the permanent listings with a storefront which are not searched with the regular search index), you have to pay a monthly fee for the service (anywhere from $16 to $500 a month, depending on the tier of service & extra features, etc.). In addition, you always have to pay a small insertion fee (much smaller than you would with a traditional eBay auction listing, since it's not in the search index and doesn't get near the traffic as a regular auction), and then you also pay an end of transaction fee which is a percentage. Lol, and then of course if they pay with Paypal, there are the massive Paypal fees, and since Paypal is owned by eBay, they're getting their chunk there too, lol.
Here are the current fees for regular auction listings:http://pages.ebay.com/help/sell/fees.html
and here are the current fees for eBay store listings:http://pages.ebay.com/help/sell/storefees.html
With a regular eBay auction, you pay just the insertion fee and the end of transaction fee, with no monthly fees, but the insertion fees are much higher.
The fees add up - I have a store and I list regular auctions as well, and if I sell $7000 that month on eBay I typically owe eBay about $500-$600 dollars in fees. Which of course, is much less than the commission I'd pay a gallery for example, but it's still pricey.