The media bias for Ron Paul seen mostly on the internet is simply an extension of his supporters' fervor, and their widespread use of the internet as a fundraising and publicity tool.
The bias against Hillary probably stems more from laziness than anything else. We already know quite a bit about her, so it's easier to play up her shortcomings than digging into Obama's past. As news agencies try to deal with the media shift from television and print to internet publication, this will probably get worse, and seem much more so due to the repetitive nature of the net. The "cut and paste" syndrome we see happening so often with blogs and news collection sites.
I'm in agreement with the Obama snafu being more concerning, if only because he'd used his affiliation as a Christian several times in the past, and now, when it's disadvantageous, he pulls a sneaky word game with us, declaring that he doesn't really pay much attention to what his pastor says, but still includes him as a friend. If you're not listening to your pastor/reverend/rabbi, etc., why are you going to a church? And why affiliate yourself with a religion when you don't follow the dictates of your cleric?
Hillary, at least, is fairly transparent as far as such things go, and we've seen her husband, presumably with her influence, do good things for the country, and others, including a rather nifty
trade agreement with Cambodia, which made Cambodia one of the more human-rights friendly manufacturers of low-cost goods, and went unrenewed and expired in 2001 (as far as I remember).
Obama is more of an unknown, and as such, is probably better suited to a Vice Presidency, where his influence will be heard, and he can also get a more hands-on experience in the White House, leaving him ripe for election in 2012 or 2016.
My fave, now that Ron Paul is out of the running, would be a Clinton/Obama run, I'm rather sad to see that the politics of campaigning have made this a seeming impossibility. And, unfortunately, if what I've heard is correct (Hillary offered a VP slot, Obama turned it down in favor of Richardson), it makes me more suspicious of Obama's ability to do the sort of compromising that is necessary, and desireable, in U.S. government.