Many voters voted against Trump in 2016 and it didn't hurt the GOP. Republicans down ballot didn't benefit much in areas where Trump greatly improved over Mitt Romney and weren't hurt in many areas where Trump underperformed Romney. Voters didn't associate Trump with congressional Republicans as strongly as voters have in the past. Republican congressional candidates actually got more votes than Donald Trump. That didn't even happen for Democrats in 2008 even though they got a higher percentage of the two party vote than Barack Obama.
Democrats got walloped in both of Obama's mid-terms. The last time one party had two mid-terms where they did at least 3.5% worse than they did in the Presidential years was the GOP in 1970 and 1974. That was a time when the south was so heavily Democratic that Republicans barely competed. Democrats had a systematic advantage in the House vote. Do Republicans have one in mid-terms now? Maybe, although it's likely that they don't.
While voters didn't strongly associate Republican congressional candidates with Trump in 2016 they may not be able to escape that in 2018. Before Trump was an outsider but now Trump is in government, right alongside congressional Republicans. Congressmen don't usually oppose the President if he's from their own party and even when they do people don't always pay attention. Most people see Donald Trump's immigration order. How many know which Republicans oppose it?
Donald Trump has already gotten the opposition mobilized against him. It took Barack Obama months to get this level of opposition to him. As the Tea Party showed a motivated opposition wins elections. If Trump keeps doing things that stir up this level of opposition Republicans will pay a price.