Because the moment someone offers something for free, it's met with suspicion. Windows Phone licenses are not free and iOS doesn't even have licenses. But Google gives away Android with no license fees required. And somehow that makes them less than legitimate.
Yes, the Open Handset Alliance exists, and yes, Google has an agreement with the OEMs who choose to receive Android from Google. It's no less damning than any agreements a Windows Phone licensee would have to agree to, an iPhone 3rd party hardware (like a charger) manufacturer, etc. The difference is the initial cost: nothing.
There are accusations that Google promotes their own services on Android. Absolutely, as do all the other mobile phone platforms. Windows Phone comes with Microsoft apps aplenty. iOS actually forces you to use their apps by default, if you click a link from email, it opens in Safari, no matter what other browser client you have installed. From a user standpoint, Google's additions are no more or less restrictive than their counterparts. None of Google's behaviors regarding Android are much different than how Apple or Microsoft treat their mobile platforms, except one.
Somehow, without something like a license fee, I think most look on Google's agreements as something less than a business transaction. They are cruel restrictions placed on an otherwise flexible product, iron chains that restrain the great freedoms of the OEMs, who chafe under the strict yoke of Google. None of this is true, it is merely perception, a perception that begins and ends with the lack of licensing fees for Android. If Google charged $5 per Android license install, none of this would be a problem.