I personally prefer to create the hbm.xml files myself. I've used Fluent, but I just like managing the nitty gritty myself for things like this. However I've not run into any mappings that I haven't been able to get working with Fluent though...
It is my understanding that Fluent nHibernate actually creates an hbm.xml file in the background based on your settings that is in turn used by nHibernate... so being that Fluent is itself creating the mappings, I would argue that just creating the hbm.xml manually would technically give you more flexibility and access to the nuance of the mapping file...
I think that there is a similar learning curve for both, so if you are going to bother learning Fluent that itself creates hbm.xml files, why not just learn how to create the damn hbm.xml files yourself in the first place and skip the middle man!
Unless you are doing MANY MANY projects in rapid succession, the act of actually mapping your database is only a fragment of the actual work you are doing on a particular project.