Since Wakatobi Dive Resort is not on a public boat route, if you want to fly to Wangi Wangi and take a boat over, you would need to charter a private boat. It's my understanding that to charter a private boat from Wangi Wangi to Wakatobi will cost at least $200 each way (you have to bargain, and it could cost much more), so yes, you're looking at a minimum of $400 for boat charter plus your flight to Wangi Wangi, plus whatever porter service you need.
Wakatobi Dive Resort is not a budget option, and the charter flight isn't a budget trip--there's no weight limit on baggage, you are ushered through the whole airport on arrival at Bali from your commercial flight (including VIP assistance through immigration and customs) and on departure from Bali to Wakatobi (including lounge access), and you land at a private airstrip to go to the resort. If you are looking to save money on the cost of the flight to dive in the Wakatobi area, you would be better off going to a different resort. There's one that's an upscale place offering airport transfers between the Wangi-Wangi airport and the resort. There are also less expensive options for dive centers on Tomia and Hoga, and those will advise you on the ins and outs of travel to the islands.