One of the key differences between those two kinds of races is the power of incumbency. Outside of wave elections or significant personal misconduct, congressional incumbents are notoriously difficult to dislodge. In 2016, about 97 percent of House incumbents on the general-election ballot won reelection. In the wave year of 2010, the House reelection rate slipped down--to a mere 85 percent. House incumbents can often blow out their challengers with higher name recognition, overflowing campaign coffers, and a seasoned political team. This leads to a situation where, in a presidential election year, House incumbents often do better than their presidential counterparts in a district. When a political party has a majority in the House, that advantage is compounded, leading to a situation where the majority party in the House gets more votes than its presidential standard-bearer.
It's hard to compare House and presidential electoral performance over an extended period of time because, in recent decades, House elections have become much more tied to presidential politics. Ticket-splitting still lives, but it is much diminished from the middle of the 20th century. That caveat aside, over the last twenty years, the majority party in the House usually performs better than its presidential nominee.
In the chart below, I give the raw popular-vote percentage followed by the margin in parentheses:
House Republicans: 48.2 (0)
Bob Dole: 40.7 (-8.5)
Difference between margin of majority party and that of nominee: +8.5
House Republicans: 47.6 (+0.5)
George W. Bush: 47.9 (-0.5)
Difference between margin of majority party and that of nominee: +1
House Republicans: 49.4 (+2.6)
George W. Bush: 50.7 (+2.4)
Difference between margin of majority party and that of nominee: +0.2
House Democrats: 53.2 (+10.6)
Barack Obama: 52.9 (+7.2)
Difference between margin of majority party and that of nominee: +3.4
House Republicans: 47.6 (-1.2)
Mitt Romney: 47.2 (-3.9)
Difference between margin of majority party and that of nominee: +2.7
2016Now, if one wanted to be truly rigorous about this whole comparison, one would have to take some further numbers into account: the size of the House majority heading into the general election (the bigger the majority, the bigger the compounding advantage of incumbency), the number of vacant and non-contested House seats, and the rate of House-race nationalization.
House Republicans: 49.1 (+1.1)
Donald Trump: 46 (-2.1)
Difference between margin of majority party and that of nominee: +3.2
Nevertheless, the back-of-the-envelope chart above suggests that, relative to House Republicans, Donald Trump performed better than Barack Obama did relative to House Democrats in 2008. Democrats had a smaller majority heading into 2008 than Republicans did heading into 2016, which suggests that House Republicans in 2016 had a greater incumbency advantage than House Democrats did in 2008. If you're looking for evidence that Trump was radically weaker than a generic Republican candidate, the overall House vote might not provide it.
As with Senate elections, House elections have a baked-in power of incumbency, which is one of the reasons why trying to compare the performance of incumbent members of Congress to presidential candidates is a tricky enterprise.