From my experience I would say always donate to the shelters, charities, programs, and food banks.

There are a lot of different kinds of "homeless" and we don't see 99% of them

The people you see on the streets are (typically) either addicts, have a physiological disorder, or are professional "homeless". These people make up a very tiny fraction of homeless but are more 'in your face' so they are the common 'stereotype' of a homeless person, which couldn't be further form the truth.

The Addicts will use the money for their fix, if you are cool with that then fine, but it's not really helping anyone. For these people to get off the street the need to hit rock-bottom, and if being homeless isn't rock-bottom then they may not have that in them. Even for a millionaire, addiction is a personal struggle and there is almost nothing anyone else can say or do to get an addict to stop.

If someone has a physiological disorder and they are homeless there is a good chance that they are an addict as well, but if they are not then some money for food can help. In most cities in the US there are places for the mentally 'disturbed' to go, but you cannot hold them there against their will unless they are an "immediate threat to themselves or others" meaning that there is a place for these people but since we cannot legally hold them, they chose not to be there. So in this case, giving to a shelter or program that specifically helps the homeless with physiological disorders will help 1000X more in the long run than simply giving one specific person a few dollars.

Then we have the professional homeless, fuck them,

Then there is the vast majority of homeless people, you don't see them begging, and when you do see them you don't even know that they are homeless. Hell, you probably interact with a few homeless people a week and never even know.

These are the people staying with friends, living in their car, bouncing from shelter to shelter, working (yes, a lot of homeless people have jobs), or otherwise trying to make their life better.

When you donate to shelters and programs, you are helping the homeless who are already helping themselves. You are helping them find employment, get counseling, and most of all you are helping them get a home. Whether it be through habitat for humanity, or a charity that helps and teaches people how file for section 8 housing. These programs do so much more than give people a hot meal and a bed, they actually help people return to society and live normal lives.

Remember that 99% of everyone who becomes homeless, eventually get back on their feet. And for many of them the biggest factor for them getting 'back on their feet' is the charities, churches, programs, and shelters. Not the $2 you gave an addict on the side of the road.