I just bought a 2001 Mazda Protégé ES (a sedan, but essentially equipped the same, with 4 wheel disc brakes and 16 inch rims with 50-series tires).
I tell you, it?s a blast to drive. I love it! The ride is a little harsh, I suppose, and the engine runs a bit too fast on the highway due to its sporty gearing (~3400 RPM at 70 MPH in fifth gear, IIRC), but WOW, that handling is great. The current Protégé reminds me of what Honda Civics used to be, pre-92, when Honda made some of the sharpest handling ?ordinary sedans? on the road.
I don't have experience with the Matrix, but because it's a Toyota, I'd expect it to be a little more comfortable than the Protégé on long trips. Do you want a car with extra-sporty handling, or a more comfortable cruiser? Think about that, test drive 'em both, and then decide.