I always thought some dogs are just more timid/shy than others.

sometimes they are timid but most often dogs are abbused because people dont like what they are doing. Some people can only refer to violence. When they do that the dogs get scared of people.

Shelters and Rescues typically pick up animals that are not in good living conditions and/or have been abused, this is why they are there in the first place. Very rarely do they have new puppies and litters just because.

Because of this many people know most of the animals in these have either been surrendered by their owner or have been taking out of an abusive home.
However, just like SOME people make an assumption that "all dogs are abused" you are making an assumption saying "everyone assumes.. blh blah".

There ARE of course other reasons, new environment, out of place not used to being in ahome, ect. But its a majority of the animals and the reason they are there that make most people assume they were abused

your definition of abuse might be different from others. a dog that gets slapped on the head may be headshy and not like being petted. a dog that gets screamed and yelled at all the time might be nervous and anxious.
it doesn't necessarily mean someone beat the crap out of them with a 2 x 4.

Not everyone assumes this.

I wouldn't assume that. It's loud and unfamiliar in a shelter--that could make almost any dog a bit fearful.

I've never assumed that. I didn't know others did.

A lot of shelter dogs just haven't been socialized.

People associate the fear in the dog to be caused by an abusive owner because they can no longer true humans. Though this is not always the case.