This has typically been the case for probably close to a decade now. At some point around the P4 extreme days (iirc) they made a business decision to stop getting utterly killed by Newegg and Tigerdirect. There was a lot of talking on the various enthusiast boards about it at the time whether or not it was going to be a good long-term move.

The loss-leader strategy appears to have worked! I typically try to buy from Microcenter now when possible, and I almost always give back that $50 cpu/mobo combo savings in margin on the rest of the build (and then some) simply due to convenience.