My expertise lies more in what to do AFTER you've established this link.
Filemaker has a PHP API library, however the documentation is choppy, and the PHP itself is obfuscated. There's a lot of questions you'll run across that you have to figure out entirely for yourself. (Like how to differentiate between AND and OR in your queries, how to do IN-style queries, etc.) I've figured this all out the hard way.
FileMaker isn't designed to replace a standard SQL database - it's an entirely different beast. Think of FileMaker like Microsoft Access. You design your layouts and data in FileMaker and people in your organization connect to it USING the FileMaker Pro application.
However, eventually you want to be able to make some data in FileMaker available over the web. Perhaps you want to publish a schedule on your website and that schedule resides in FileMaker. Or maybe you want people to be able to submit contact requests from the web, and have that start a new project in your issue-tracking FileMaker database.
I have to agree here, having worked with Filemaker previously. However, it really does shine for small business type applications where you need to set something up in a hurry, have only a handful of people using it and they're not very technical. Once that business grows though (eg. they need SQL/Web access) then you're better off migrating to something else.
However, that seems to be EVERYONE's experience, which makes me think that it's a good spot to become an expert in, since nobody else wants to go through and learn it.
I am also curious about the benefits of filemaker over a standard sql database(mysql, postgresql, and sql server or oracle if you want to pay for it)?