Congressional approval ratings are never particularly high because they don't have a bully pulpit, each one was elected by a small fraction of the country, and Congress is oppositional by design. A president, by contrast, was elected nationally, can speak unilaterally for the executive, and will usually have a celebrity factor that Congress will never have. You just can't expect Congress to have comparable approval ratings to a president.
Also, you should take into account that many of the Republican voters who elected a majority Republican Congress dislike Congress because they think they aren't opposing the president strongly enough. Democrats, since Congress now has a majority of Republicans in both houses, are naturally not going to like Congress right now. So, again, you can't look at the difference between Congressional approval ratings and Obama's approval ratings as a sign that people like Obama's policies.
What's interesting about Obama is that he's remained relatively popular even while his policies have been unpopular enough for his party to lose majorities in Congress. He's a personally attractive guy who knows how to use the media to get his message across. And his team has done a good job of insinuating him into pop culture, even if you think that's not what a president should be doing. So people find him hard to disapprove of, even if they don't particularly like the things he advocates.