I routinely use my Garmin eMap during flights, and have never been told to turn it off. Several flight attendants have asked what it is, and several have asked jokingly "Are we going the right direction?"
The 2-dimensional locator is quite accurate, but you can't get a lock on enough satellites from the tiny window to get an accurate elevation. 35,000 Feet often varies by 500 feet or more.
The inflight maps tend to only show wide area maps. You still need a GPS to know what a particular road, town, or river is.