Very basically, most used it to conveniently mule using one computer.
The problem is not that it's an unfair advantage. It breaks the ToS, plain and simple. How did people NOT see that red text that said:
"Usage of third party software may result in account closures and/or suspensions"
Or something like that. It had been there for a month! People thought it was an empty threat and laughed while the other users lamented about the insane bot usage and hacking. There were thousands of bots spamming games and farming items. I'm sure that trading sites use d2loader to facilitate transfers and to cut down on the number of PCs they need to use. And these guys were all hit with Warden's big digital double-upped Steeldriver. I just wish that those other programs used by bots had also been crushed.
Now, I do understand where you're coming from. I'd be angry too, but the warnings had been there, and if you want to play on battle.net, you have to abide by the rules. If I were in your shoes, when they restore my CD key and I still feel like playing on battle.net, I'll abide by the rules. If not, I'll find some server that doesn't mind me using 3rd party software.