You can generate GMP pretty well doing side ops, but resources, in particular, are a major grind right now.
Let's talk some numbers:
When in the field as Snake, you can come across resources like Fuel. Each one gives about 100 units of that resource. Where I am now in the game, it costs 18,000 units of fuel to expand ONE strut in Mother Base.
There are Combat Unit missions that specifically give large quantities of these resources (~4,000 per mission). As far as I can tell, this is the fastest way to get this stuff, and with only two units available to deploy at any time, it's gonna be a while before I max out anything.