Apple has a long history of completely disregarding the needs or desires of accessory manufacturers, and only started the MFi program after years of categorically responding with cease-and-desist letters. The program is primarily in serving Apple's interests in a level of reliability in the accessory ecosystem; it's an absolutely insignificant revenue stream.

Is this really the case? They certainly seemed to stick with the 30 pin connector for far longer than they had any reason to other than the massive third party accessory/dock/speaker market.

Because they are the ones that support Apple's products and pay a license to do so. If you change standards every Monday morning then these manufacturer would have to retool their products which would no doubt cost them.