The world has changed since then. Ads are accepted everywhere an enterprise user goes, including, in many cases, Web applications. There’s no reason why mobile apps should be any different. If it’s a tool that you and your employees need, if embedded ads make it financially viable for the developer and affordable for you, and if the ads aren’t too obnoxious, there’s little to complain about.
And if you’re an enterprise developer or a commercial software writer, well, advertising is the way to go. It seems that customers will put up with both paying for software and seeing ads. If they’re happy, you should be too. As we said in 2000, it’s an ad, ad, ad, ad world.