As the scope of the open Web has expanded we've run into many hard issues such as DRM, support for patented video codecs, and applications needing APIs that increase fingerprintability. These issues are easily but incorrectly framed as choices between "principles" and "pragmatism" --- the former prioritizing Mozilla's mission, the latter prioritizing other things such as developer friendliness for the Web platform and Firefox market share. This framing is incorrect because the latter are essential components of our strategy for pursuing our mission.
For example I believe the optimal way to pursue our goal of unencumbered video codecs is neither to completely rely on platform video codecs (achieving nothing for our goal) nor to refuse to support all patent-encumbered codecs (in the current market, pushing almost all users and developers to avoid Firefox for video playback). Instead it is somewhere in between --- hopefully somewhere close to our current strategy of supporting H.264 in various ways while we support VP8/VP9 and develop an even better free codec, Daala. If we deliberately took a stance on video that made us irrelevant, then we would fail to make progress towards our goal and we would have actually betrayed our mission rather than served it.
Therefore I do not feel any need to apologize for our positions on encumbered codecs, DRM and the like. The positions we have taken are our best estimate of the optimal strategy for pursuing our mission. Our strategy will probably turn out to be suboptimal in some way, because this is a very difficult optimization problem, requiring knowledge of the future ... but we don't need to apologize for being unomniscient either.
A related problem is that our detractors tend to view our stance on any given issue in isolation, whereas we really face a global optimization problem that spans a huge range of issues. For example, when developers turn away from the Web platform for any reason, the Web as a whole is diminished, and likewise when users turn away from Firefox for any reason our influence of most issues is diminished. So the negative impact of taking a "hyper-principled" stand on, say, patent-encumbered video codecs would be felt across many other issues Mozilla is working on.
Having said all that, we need to remain vigilant against corruption and lazy thinking, so we need keep our minds open to people who complain we're veering too much in one direction or another. In particular I hope we continue to recruit contributors into our community who disagree with some of the things we do, because I find it much easier to give credence to contributors than to bystanders.