I think that customers are going to focus on the "fit and finish" of your product, not what platform it's running on. If you write it in ASP.NET, most Microsoft-based businesses will be able to run it, as well as any non-Microsoft-based businesses that use Mono.

Just make sure to test your app on both Windows Server and a couple of flavors of Linux/Mono, and each of those combined with the major database vendors (MSSQL, Oracle, MySQL, PostgreSql). If it works well with all of those "out of the box", I think you'll have a lot of happy customers.