Hillary ran a sub-par campaign as one of the least popular candidates in recent history, and that hurt down-ticket races. The democrats made a strategic mistake by allowing Clintonistas to take over the DNC and party establishment to the point that she was essentially "the anointed", and faced no real competition. Had e.g. Biden or even Franken run, the results might be quite different. Heck, if Obama had run against Trump (for a third term, were such a thing possible) it would likely be a different story. This is not the whole situation, of course; e.g. districts are more gerrymandered than ever, reducing competitiveness and allowing party establishments to push their favored candidates (out of touch establishment = unpopular candidate); e.g. the last congress was the most dysfunctional in decades, meaning that the bills that made it were compromises, and not a full test of democrat ideas; media echo chambers have polarized voters; etc.
As easy as it is to critique Obama's policies on privacy & foreign policy, he was assured and rational, which people like in a leader. It's entirely reasonable that there's such a wide gap in approval polls. There's really no reason to significantly doubt them.
Regardless of whether you agree on the above, we're about to see the GOP have its way and push a slew of policies that they favor. Many will actually be favorable for entrepreneurs and startups, but my guess is that overall they will turn out to be quite unpopular. I predict the house to flip back in 2018 and for Trump to be crushed in 2020 (if he makes it that far without being impeached.) We'll see.