Warning! Spoilers ahead for Wolverine: Patch #4
Many fans might think that SHIELD's helicarrier is just a cool vehicle for shield to drive, but in a recent Wolverine comic, it's revealed to that the flying aircraft actually has a pretty practical purpose.
Throughout his superhero career, sometimes Wolverine adopts the moniker Patch to hide out in the criminal nation of Madripoor. In one adventure, he got sucked into a conflict in the jungle on the outskirts of the city. A group of mutants are being hunted by several forces including Russian soldiers and the Yakuza. After first being mistaken for part of the soldiers by the mutants, Wolverine makes a quick recovery and then attacks everyone in a brutal battle to give the mutants time to escape.
In Wolverine: Patch #4 by Larry Hama and Andrea Di Vito, Nick Fury is watching the entire scene unfold from a helicarrier above the jungle. Wolverine is doing such a good job at eliminating all of the soldiers that the various groups, which are flanking the area from multiple sides, are firing indiscriminately into the jungle. The stray bullets are even hitting other groups. There's so much collateral damage going on that Nick Fury and SHIELD have a massive strategic advantage by having a base of operations above the conflict rather than inside of it. This way, they can monitor the scene in real time without fear of being caught in the crossfire.
Of course, the helicarrier is a huge asset for being an operating base that can travel anywhere in the sky. But this ability to be close to a conflict yet safely out of reach of any harm is a huge advantage for SHIELD. Nick Fury is primarily a spy, not a soldier. This means that he works more with intelligence, reconnaissance, and information gathering than anything else. Being able to hide amongst the clouds while also being directly on top of a hot zone is incredibly helpful for someone that wants to see how a situation unfolds before getting involved.
Of course, the helicarrier isn't a foolproof vehicle. They have been attacked from time to time and they aren't the most inconspicuous mode of transportation. But the conflict with Wolverine wasn't an all-out superhero brawl that might be taken up into the skies if there are any flyers involved. The skirmish Wolverine was involved in was primarily an on the ground battle with non-powered individuals. In that case, the helicarrier can be utilized greatly and SHIELD can do what SHIELD does best, which is spying on dangerous individuals.