The usual drawback for using .net was the difference in cost compared to using an alternative like php/ruby,but their are cloud hosting alternatives for .net now so it seems that drawback is changing. Likewise as the others have mentioned, if your co-founder is wiz at it,then go for it, you can always change and iterate later.
I'd say, that drawback had changed drastically over past 3-4 years. Website Spark, BizSpark minimize licensing costs during the startup phase. If business picks up, the cost of software will not be an issue anyway, otherwise both programs do not have any sort of "exit costs". As for hosting - there's plenty of affordable options right now.
