I used to work for an online retailer, and as you say there are vultures out there, and some badly run companies. You see complaints from a few people on here but how many people every day buy a car from an online company and are happy with it and don't post anything. The company I worked for sold upto 50 cars a week and the majority of these customer were extremely happy and reccomended us to their friends/family etc. I think you will find that the vast majority of people buying a car over the internet when dealing with the right company have a good experience.
If you can get the same deal from a dealer then there is no question - buy the car from the main dealer for piece of mind. Although in the present climate are you any safer buying from a main dealer? there must be a few of them on the brink of going under. Horners, For example, Skoda in Manchester I think it was recently where customers turned up to collect their cars and everything had gone, the company I think had gone into liquidation. There will be many more main dealers that are on the brink of this happening.
Buting a car over the internet, is quick, easy, no haggling with pushy salesmen to be done as the companies usually offer best price first time.
Regarding the pricing, with some brands you will be able to haggle and get the same deal from a dealer, with others, you might find the internet company gets you a fleet discount you are unable to obtain walking into a showroom yourself.
Either way, pay your deposit on credit card, then you are covered under the consumer credit act for the deposit and the balance.