The 2004 popular vote numbers in the House are nearly identical to the 2002 popular vote numbers in the House. Notice the similarity to the popular vote for President in 2004.
2004 numbers: Reps. 51-Dems. 47
2002 numbers: Reps. 51-Dems. 46
This lies in contrast to the 1996, 1998, 2000 House popular vote numbers which were tied at 49-49 for each election.
There has been a shift since 2000, it seems obvious now.
Whether this has to do with 9/11 or the strength of Bush's politics is still up in the air right now.
But much of the 51% the House GOP won is concentrated in different areas to the 51% that Bush won. The similarity is really only the topline figures.
---
Re: higher turnout... I think this election was unusual in that there was a higher than usual evangelical turnout as a result of Gay Marriage etc. being on the political agenda.
There was also a higher turnout of non-evangelical voters (not in relative terms though) and if there hadn't been I think Bush would have won by as much as the media over here acted like he did (there coverage was hysterical and acted as though he'd won a landslide).
Turnout is a relative thing I suppose. Like pretty much everything else in politics.