I think geoffc is correct. It's primarily about cost and if that is a major concern then Hydrogen is almost immediately off the table. It is good for high efficiency upper stages but as both other answers mentioned it's bad for a lower stage as the thrust is on the lower end and the tanks are heavier. You need a pretty advanced engine just to make a Hydrogen first stage possible without boosters to help out.
You could still do a Kerolox first stage and a hydrogen second stage but that has added costs too. As Geoffc noted you have added cost from the ground systems at the launch sites and extra costs for development of the two different types of engines but for SpaceX it goes beyond even that as they have significant similarities between the first stage and the second stage. On top of using the same engine which the are producing in relatively significant quantities for rocket engines (~150 last year for the launches they performed) the two stages are also the same size and use the same tank designs so they can share tooling and their construction is largely similar. This helps drive some economies of scale and improve efficiencies of the assembly process instead of needing two sets of tooling and processes for assembling two completely different types of tanks.
Additionally you have to look at how the rocket as a whole works. The F9 first stage shuts off relatively early compared to other rockets so it is lower and going slower than say an Atlas or Delta first stage when its done its job. This ends up working well for recovery but means that the second stage has to do a lot more. It's quite a bit bigger than most other second stages and has a lot more thrust. A hydrogen powered F9 second stage would require much more powerful engine than the typical RL10 or possibly multiples to get the thrust needed.
The second stage would also need much larger tanks than a delta or atlas second stage or even the current F9 stage. The first stage is already at the limit of what is road transportable, any bigger round and it won't fit under overpasses and any longer and corners will be a problem so you can't really push it any further even you can still handle recovery. Making the second stage bigger to handle the hydrogen tank needed might start bumping into the same limitations on size that the first stage hits. The entire rocket as a whole is already really tall and skinny and going even taller and skinnier would also be difficult.
Road transportability is important for cost too and critical to the way they are currently setup. The rocket is built in California. Sent to Texas to be tested. Then to Florida or back to California for launch. That gets much harder and more expensive if it isn't road transportable. Larger rockets are typically built near the launch site (BO is building the New Glenn in Florida right near the launch site) or near the water like the BFR is being build at the Port of LA.
You also have to keep in mind the history of SpaceX and the the F9 itself. SpaceX isn't the first rocket company startup but they are the first to really be successful. Many others failed and went bankrupt and SpaceX was very close to following that same path. Go back to September 2008. They've failed at their first three attempts at launching the Falcon 1. Musk has scrapped together enough money for one more attempt at launching the Falcon 1 before they go bankrupt. Everything is on this launch and if it fails SpaceX will go the way of countless other rocket company startups but hard work and perseverance pays off. Their launch is successful. Their business plan at this point is to launch smaller payloads on the Falcon 1 to hopefully fund the company while working on improving the Falcon 1 and eventually building a Falcon 5 and Falcon 9 to launch progressively larger payloads. Jump ahead a couple months to the end of 2008. NASA has awarded you a contract for Commercial Resupply Services to deliver cargo to the ISS. Your old plan is out the window you need a much bigger rocket. You need to get the F9 going and doing delivery runs to the ISS ASAP in rocket development timelines. That means you reuse as much as you can and you certainly don't have time to design a whole new hydrogen engine for the upper stage.