My frustration with Apple has been fairly well known. I've blogged about it numerous times over Section 3.3.1.
Now, I'm frustrated that Apple has Section 3.3.1. I was frustrated yesterday, today, and will probably be frustrated tomorrow. Having said that, up to the time of this writing, I'm not familiar with any apps that have been banned from the Apple iPhone App Store due to their being written in MonoTouch. Why? I'm not sure. Only Apple can answer that. My guess is that because MonoTouch allows devs to build apps that run natively on the device, its viewed as ok.
Will apps written in MonoTouch still be allowed into the App Store? I have no idea. My guess is that if MT becomes really popular, Apple would be concerned that another company is controlling its destiny and might change, but remember, this is only speculation. At the same time, remember, the Apple post on Flash is about Flash, not MonoTouch, PhoneGap, or anything besides Flash.
Maybe the blowup (mine and others) was over nothing. Let's stop and see what happens over the next 6-9 months. Right now, today, MonoTouch apps are being accepted. Let's focus on that