One thing to remember is that it isn't always the same group of aliens invading, and they have used a decent variety of tactics. For example:
Xilliens (IoAM): Captured King Ghidorah, but had monitored his first attack on Earth and knew that Godzilla and Rodan could overpower him. So they captured Godzilla and Rodan as well, and used all three monsters to invade Earth, supported by their warships. This was a fairly well-researched plan, and may well have succeeded if the inventor dude hadn't accidentally discovered their weakness to sound.
Killaks (DAM): Haven't seen this movie in years and don't remember it well, but using ten of Earth's monsters to attack certainly seems like a good base concept.
Nebulans (GvsG): Attempted to use Ghidorah and Gigan, supported by Godzilla Tower, to overpower G and Anguirus. If memory serves, this would've worked if the human characters hadn't sabotaged the Tower at the last minute.
Simeons (GvsMG): Built an extremely powerful anti-kaiju weapon, Mechagodzilla, to wipe out G and any other monsters that got in its way. Would likely have worked if Godzilla hadn't suddenly turned into freaking Magneto. And, of course, the Simeons had no way to plan for that, and can't be blamed for losing to it.
Simeons (ToMG): Used Mechagodzilla again, supported by Titanosaurus. Came close to working, but was sabotaged by human characters.
So really, it seems like the aliens underestimate humanity more than Godzilla. In all but one of those cases, it was our intervention that saved Godzilla. And we are a formidable enemy fighting on our home turf, while they're thousands of lightyears from home. Combine that with some understandable arrogance on their part, due to the technology difference, and our beating them isn't hardto beleive.
"You know it's good advice when you're still confused afterwards." -Michelangelo