Generator wiring: I have a new honda generator. I ran 3 wires from the garage to the transfer switch in the house. When I start up and throw in the breaker on the generator, its GFCI trips immediately. It is a long run (125ft) run to the house and I used heavy wires. But I only ran 3 (blk, red, white). I connected the green to another grounding conductor between the house and the garage. Is this what is wrong? What else could it be?

The connection from the generator to the transfer switch needs to be 4 wire.
That being said, what is amperage of your generator, and what do you consider heavy wires? That's a long run.

You also need to break the ground-neutral bond at the generator.
There has to be only one point where the ground and neutral are bonded. You have two points. The generator and the house.

Being 125' away, I'd install a ground rod at the generator for safety.

And I'd also run an insulated ground.