Tamiya does far more to try for scale appearance than Traxxas does. This takes time/effort/money. I think Tamiya is higher quality (personal opinion), and they include the best kit instructions I've seen. Traxxas doesn't do kits, so no instruction costs.
There are other factors I'm sure we don't know. How does Traxxas pay it's labor compared to Tamiya? Stuff like that.
In general though, it's easy to find an RTR by brand X and compare to a bare bones kit by company Y and wonder why the RTR is cheaper. It's not just Traxxas vs. Tamiya.
For example, Losi has some excellent RTR deals that make you wonder about kit costs for tons of other companies.