1-They are too afraid to talk
The bandits or whoever else the bad guys are have warned the people that if anyone talks, the informant will be killed and/or the village will be burnt down. Such is the case in certain parts of Sicily, Northern Ireland or Mexico, for example. Perhaps law enforcement is either too frightened to act or heavily infiltrated or both, and cannot be trusted to support witnesses and keep them safe.
The bad guys have a mage, witch or other magic user in their ranks who has placed a geas on the local people that stops them giving information to law enforcement or anyone else about the things that they are doing, and it's a strong one. To get anyone to talk, the PCs will first have to become aware of the geas-not easy when noone can tell them about it, and then have the magical power to Spellbreak the geas so that people can talk freely.
3-They are themselves accomplices
The seemingly innocent people are not as innocent as they seem. In the case of smuggling certain items, or plundering a shipwreck, many or perhaps everyone benefits from the crime in some way or other, so they don't want the "bad guys" or the smuggled or stolen items to be found. In real life, when a ship carrying whiskey was wrecked off a Scottish Island and plundered, law enforcement met with a wall of silence from everyone about the location of the missing whiskey.
4-They don't trust the PCs
They don't trust the PCs. Maybe they think the PCs are corrupt; maybe they think the PCs are spies sent by the bad guys to uncover snitches; or the area does not like strangers.
5-They themselves are going after the offender
Unknown to the PCs many of those who they talk to are a secret band of vigilantes who, fed up with the activities of the bad guys, have decided to get together and mete out lynch law on them. If the PCs have been ordered to take the bad guys alive for trial, the vigilantes will not give them information, as they want to get to the bad guys first to mete out a bloodthirsty revenge. Historically, many bad guys and even suspected bad guys in the West ended up strung up by vigilante bands. Some of these vigilantes became de facto bad guys themselves.
6-The bad guys have a hostage
The bad guys have one or more hostages from the area and have threatened to kill or maim them if anyone gives any information about them to the PCs or to anybody else. That is generally enough to keep most people silent.
7-One person's villain is another person's hero or heroine
Famous figures like Robin Hood, Jesse James, and Pablo Escobar are not seen as bad guys by everyone. If their targets are widely seen as rich and greedy, like the big banks, or they give at least a small amount of their ill gotten gains to the poor, or both, then they can be seen as the good guys by a surprising number of people. Certain kinds of bad guys have a romantic image about them, which they normally, but not always, don't deserve. Many people can sympathise with the criminal on the run, if his or her crime is not considered too unpleasant or brutal. Maybe the bad guy helped people find jobs, both legal and illegal. Maybe the bad guy intimidated landlords into not evicting their tenants-and the tenants are now the bad guy's strongest supporters. Maybe the bad guy is genuinely innocent and was framed. The divide between good and bad guys is not allways black and white.
Additional Ideas (1)
Some people just don't want to be involved. Potential witnesses slam doors in faces. People think they're above it all, not part of events. This might overlap with fear, but really, there's an element of apathy in this attitude, an inertia that can be very hard to overcome.