Typically you reflash at the dealer because there is a problem that they've been able to fix with software.
However, if you're not suffering from a problem, I'd leave well enough alone.
Subaru has a campaign going right now for all 2. 5 liter non-turbo cars from 06-10 to reflash because they've done something that will light up the catalytic converters and sensors faster to improve cold start emissions. Because it's emissions related, it's mandatory - failing to get the flash done could be considered owner neglect should a warranty concern come up.
Do you know anyone who owned a v8 Ram pickup back in the late 90s? Search google for "ram death flash" if you want to know the worst case scenario for a factory flash... Owners were getting detonation due to (imho) leaking intake manifold baffle plates causing a lean condition, and Chrysler's infinite wisdom was to reflash the ECM and pull a TON of ignition timing. After getting the flash, owners complained of a noticeable loss of power AND poor fuel economy. Chrysler's only solution? Buy a Mopar Performance aftermarket ECM for several hundred dollars, and then run premium gas forever.
I'm of the school of thought (with my personal vehicles) that factory programming is best left alone if it's not broken. Aftermarket programing will get you better performance and better economy.