What are the actual benefits of using hydrogen as a fuel source?

To understand energy, you have to look at economics.  The market is driven by one thing, profit. The grain of rice, the pot you cook the rice in, the water that is in the pot and the heat source are all using energy and therefor have a cost associated with it.  In theory, the beauty of the market is that it selects the most efficient producer and that drives innovation.

The problem is that it does not care if the energy used to make products is slave labor, the energy source is polluting (which is an external cost),  or green energy, it only cares about generating the largest profits, it would be delusional to think about it in any other way.  Any ethic consideration has to be enforced by legislation.

Now we get to hydrogen as a form of energy, as usual, there are multiple issues at play.

Hydrogen stores a lot of energy and it burns relatively clean, so it would satisfy the environmentalists as a energy source.  The problem is that electrolysis is inefficient and as a result today 95% of the hydrogen made today, is made by  steam-methane reforming.   Ironically it would actually be more efficient to use the methane as the fuel so it is just a marketing technique.  And many of the people promoting it are funded by the fossil fuel industry.  It is a marketing ploy that breaks the free market as the consumer is not making an informed decision.

With renewables, there will be shortages, but the best way to reduce those shortages is to add more renewables,  It is already common to over-panel solar installations, as solar panel are now only 25 cents per Watt.  As we keep adding renewables there will be times when there is a surplus of energy, the power company might not be able to sell it, so you could consider that "free" electricity.  They could decided to make hydrogen using electrolysis with this "free" electricity and either use the hydrogen to generate electricity during peak demand or sell it on the open market.  It is important to remember that while much cleaner,  renewables are not exactly green either and this is something that will need to be addressed (with legislation) as well.

Over time, I expect that hydrogen will become a clean and cost efficient source of energy, It will take some time (20 - 30 years) to get there.

The way to think about it is that hydrogen isn't a fuel, but an energy carrier. You use energy to extract it, what you're producing is potential energy that can be moved to where you need it, and can then be converted to heat or kinetic energy at that different point.

It's really no different in concept to batteries. Your plant might require more energy to produce batteries than they'll ever give back, but you sell them at a profit because people want portable products. No one cares that the process isn't 100% efficient.

One advantage of hydrogen is that much of our fossil fuel-based technology such as combustion engines or diesel generators or heating systems require only minor changes in design to run on hydrogen (I'm not talking about fuel cells) and, since these have been mass produced for years, costs associated with those changes are minor. 

If we can bring the cost down of producing it, then the fact the cycle of producing and burning it is lossy shouldn't bother us because no energy distribution system is 100% efficient.

How do we power ships out at sea or tractors in the middle of a field and do it in a way that minimises greenhouse gas emissions? It's that sort of problem hydrogen could solve. If we want to use it to generate large amounts of power and have the process give us a net gain we need to use fusion.

The benefit to burning hydrogen is that it releases a tremendous amount of energy and the only exhaust is water vapor.  But as you pointed out, the downside is the amount of energy required to separate water out into hydrogen and oxygen.  But that's where renewable clean energy sources can come in such as solar and hydroelectric, which can be used to generate hydrogen which can then be used to drive engines and such.  As solar becomes cheaper per watt with the reduction in manufacturing costs, vast arrays of solar panels can be put up in very sunny places like the desert southwest, or perhaps floating arrays in the ocean or great lakes.  The energy gathered from solar can be used for making hydrogen, or putting into the electric grid for electric vehicles.