Speaking in terms of reliability, the Scion xA and xB have faired poorly. There's a rumor that Toyota rushed them to market. Of course, the issues are not related to major components (engine, brakes, tranny). To my knowledge, the Mazda 3 has many similar "quirks" as it's a new vehicle. The Protege is an extremely reliable vehicle and when the 3 gets its bugs worked out I'm sure it will be too. By the way, Ford may only own 34% of Mazda, but in Japan 34% is considered a controlling share. Ford tends to use a hands off approach with most of its subsidiaries (Austin Martin, Jaguar, Volvo, Mazda) so it's not fair to call the Mazda 3 a Ford. It would be different if we were discussing a Lincoln or a Mercury. Besides, the Chassis was built by Volvo (a good thing), the suspension was designed by Ford of Europe (a good thing) and the rest of the car is mostly all Mazda (a good thing) including the engine. The tC is obviously all Toyota and Toyota would rather start new car brands (Lexus, Scion) than buy existing ones.
Regardless, I didn't mean to open a can of worms, I was just curious if anyone was cross shopping the tC and the 3.