I use Mega, RFM69HW, SD Card in my Moteino gateways, some of which also have W5100 Ethernet on SPI. SD cards sharing SPI buses are VERY finicky. Some work, some don't, but I have found a couple of key ingredients, but, before getting into those, your original setup() set the pin mode of the radio SS but didn't write the output level high. That would be a problem.
As Felix points out, if the SD card is inserted, you MUST set the SD CS pin high before initializing the radio, even if you're not accessing the SD card.
Key ingredients:
I use the SDFat library, not the standard library.
Your SD adapter must have pullups on key pins (the reserved pins, DI, and probably CS although I'm not sure about that one as I'm not near the computer with my schematics).
You need to be very lucky! Actually, I'm being facetious here, but I'll never say I've found the magic combination. I had to fiddle until it worked and, as I said, it doesn't work for all cards, in fact, in my case, I've only had success with 2GB type I cards. Fortunately, these are fine for my GW needs, but I'll switch processors (and IDE) before I do another SD card project.
Tom