did the tech do a compression test or a leakdown test?? a fouled spark plug could cause a miss, as well as a faulty injector. so can a burnt valve (although this would be more noticeable at idle), or blown headgasket (which may or may not include smoke and overheating).
a good auto tech will at least rule out simple basics first (plugs, coils and such) and go from there. the compression and leakdown test usually are chargeable tests, but are negligable when compared to the cost of an entire engine replacement. i would ask specifics and have detailed estimates.
thre are some yahoos out there that will take advantage of the consumer, but there are some good guys out there as well. your best defense is to ask LOTS of questions and understand the answers. don't be intimidated, just be polite. if you don't feel comfortable, don't allow yourself to be forced into a repair. get a second opinion if you feel it necessary.