I used to use my HSBC debit card in the banks in the downtown area without problem but that is a couple of years ago now, so sorry not to be more up to date!!
There are three cashpoints in a small area downtown (Tamr Henna Square) close to the tourist info office ; two at banks and one just a hole-in-the-wall affair so you DO have choice if your card not accepted in one for any reason. The Bank of Oman only used to take Mastercard and not Visa, but not sure that still applies, "CIB" ATM directly opposite the info office def does take both). I find I tend to gravitate towards the Marina for sundown drinkies anyway so tend to stick to HSBC (although there is also a small CIB branch with ATM in Marina too) I now have an Egyptian HSBC account so for the last year or so haven't had to use my UK card
also don't know about charges for using other cards - but I haven't personally heard of anyone being charged
BTW you get a MUCH better exchange rate there than here and many of the shops are happy to take Euros if you happen to have any knocking about that you want to use up. Sterling is less widely accepted. Reception desk at the bigger hotels (Movenpick/Sheraton etc) will exchange travellers cheques but exchange rate V. poor!! Movenpick I believe has it's own ATM too. Dollars are also accepted in some places (note cheaper to pay for your visa at Hurghada airport in dollars rather than pounds) and we use 1$ bills for tipping as foreign coins are difficult for the staff to exchange and therefore $1 bill is the smallest non-Egyptian note you can use!! You will often find egyptians (porters etc) at the airport asking to exchange £1 coins for LE or 5 of them for a £5 note that they CAN use (it's a weeks wage for some of them). It's not a s c a m - they are
genuinely trying to convert tips into useable currency.
Credit cards are not accepted in many places - cash is rather the order of the day.