Political scientist Seth Masket ponders the Democrats' unpopularity:

Greg Koger, Matt Lebo, and Jamie Carson put out an article earlier this year showing that members of Congress get punished for voting too much with their parties. This is consistent my finding with Steve Greene that the health care vote cost supporters roughly 5 percentage points in the election and with Eric McGhee's finding that the stimulus vote and the cap-and-trade vote also took a few percentage points off the vote shares of their supporters.

Why do members get punished for voting with their parties?  

Because parties are not interested in pushing through popular legislation.  Parties have longstanding priorities (health care reform, tax reductions for the wealthy, etc.) that are molded and favored by the most active and passionate leaders within the parties.  These goals are priorities for the parties over many decades and do not wax or wane with public sentiment.  Indeed, in most cases, these priorities will run against public opinion.  After all, if everyone favored something, it would probably already be law – it wouldn't take a whole lot of energy by a unified party to press for it.

So, yes, the Democrats did suffer this year because of the poor economy.  But they also suffered because they actually used their majority to do something.

Michael Tesler takes the opposite position:

Pundits and politicians who are interpreting the midterms as a referendum on Obama’s agenda ... would be wise to read the forthcoming book of MIT political scientist, Gabriel Lenz.  Lenz convincingly demonstrates that policies subjected to intense public debate rarely become more important determinants of citizens’ vote choices.  Instead, voters will more often first pick a candidate based upon partisan and performance factors and then adopt that politician’s views about high-profile policies.  So, for example, voters who decided to vote for Republican candidates in the midterms because of the poor economy would also be more likely to embrace that party’s position on health care reform.