never did the online thing and been there probably like 20+ times, must be some new thing.
Just go straight into the "bank" counter (will look like small bank/ currency exchange type office) on the airport and ask for one, then stick it in your passport. These are the official government visa counters. Costs 25$ US - i normally get the dollars before flying to avoid the hassle. if you pay with other currency, they normally accept it too (ie GBP / Euro etc,) though exchange rate might not be in your favor, albeit usually not much.
Never been to Hurghada airport as normally landing in Cairo or Sharm, but since its a "touristy" one, one thing to look out for (at least based on my Sharm experience) - don't go to the travel company desks and ignore shouting travel agents trying to shepherd you there. They are like touts, often positioned before the actual visa "banks", luring the naive tourists in. Sure you will get the visa, but you might end up paying double
..plus last time i've been to Sharm, whole plane ran to the travel companies with massive queues, while 50 meters behind 2 bank offices were completely empty...had the visa in seconds while most ppl still queued
Also remember to fill in (ideally on the plane, saves time) and keep your landing card - immigration officer will inspect both your visa and the landing card..plenty of ppl forget one and then have to go back to fill it. After that your visa will be most likely checked again by some security type right after passing the immigration desk.
One thing to check - I would assume that Australians (again assuming you are one
) get teh visa on arrival thing but might be worth checking out your embassy page.
Flight wise - guess Hurghada is a direct one so probably easyJet or Thomas Cook etc....but depending on your times have a look at Egypt Air - they won't fly direct though and instead via Cairo, so it will take longer. Price wise might be actually cheaper, especially in the summer (but check) and there is one main advantage (at least if you book "normal" economy) - 2x 23 kg luggage...you can really take plenty of stuff with you...very useful when you are smuggling a cat tree for your gf 4 cats 
Alternatively (if you have time) is to take Eurostar and fly from Paris (or Brussels/ Amsterdam). (you can do open jaw and fly back to UK if needed) - flights are way cheaper from the continent - UK has like the highest flight taxes in the world :S
Have fun!