While the Nazis wore skull emblems on their caps

This wasn't a Nazi phenomenon. The totenkopf was a tradition from Prussian times.

Both wore black

Everyone wears black at some point or another. There isn't a military on this earth which doesn't have black uniforms in common rotation. It's a good all-purpose low-visibility color.

If they want to seem like the "true path", shouldn't they make themselves more appealing to everyday Germans

They were. The politics of how the third reich came to power are complex and well-documented, but the general gist is that Germany suffered greatly at the end of WW1, leading to the dissolution of the empire in favor of the weimar republic. This republic did what it could, but many citizens were deeply unhappy with its' performance and allegiances. Many felt that the upper class (composed largely of Jews and ex-imperials) had "stabbed germany in the back" during WW1, enabling a loss to the Allies for their own profit. In modern terms, they accused the 1% of war profiteering. Add that to the harsh terms of the treaty of versailles, and the loss of a lot of territory that had traditionally been considered Prussian / German, and it's really not surprising that a party espousing national pride and promising a return to the glory days for common Germans would be successful. Remember, the Nazis won elections fairly, and had the majority of the popular vote each time, even if they effectively dismantled the Republic afterward.

What causes these groups, who believe what they are doing to be good, to deliberately make themselves appeal villainous?

There are two different answers because the two organizations (Nazis and Daesh) are very different. Your perception of the Third Reich is entirely from the perspective of a citizen whose country has warred against it, and whose primary contact with them was on the battlefield. This is especially so because the media (and information technology in general) was not as effective in the 1930-40's as it is today - so we focus very much of the military capabilities and history of the Nazis, and comparatively less on what the voters of Nazi Germany were feeling and doing.

In Daesh's case, it's much simpler. Daesh is a state actor which is concerned entirely with conquest in the old-school sense of the word. It wants to roll into town, cut down the resistance, dominate the populace, and force everyone to bow to it. In places where there is little resistance, it offers the choice between death and paying tribute. It's been noted many times that Daesh is very good at assaulting positions, but has a less impressive record with defending them.

Daesh's image is part of this - it's constantly described as "a wave" or "a beam" or "a bolt", something that washes or rushes forward. It wants to be seen as a terrifying unstoppable force that will kill any who oppose it. When people are afraid, they cooperate. Daesh is also unique in that it uses a lot of social media to reinforce this, so it's actions are brutal and outlandish, but their effects are magnified by the sheer number of people who see them, so it's social presence is comparatively big.

So, recap, Daesh's image is part of it's military strategy.