The phrase '3-minute mage' is derogatory for the same reasons that a player that relies exclusively on cheesy rush builds in SC2 is derided.
In short: It's very effective against unprepared and unskilled players who don't know what they're dealing with. It gets you to a moderate level of success quickly and then... plateaus.
At which point, any player good enough to know what they're doing will see that said 3-minute mage has blown relevant cooldowns, use enough of their own to survive or escape, and run and hide until 20 seconds have passed and said cooldowns have faded, and then completely destroy said mage while they are exposed, vulnerable, and unable to effectively counter anything.
It's considered derogatory because the build is considered to have a low skillcap (as in, the gap between a bad player using the build and a good one is relatively small) in addition to it's relatively high skill floor (as in, a bad player with the build will still perform pretty well in some situations), and considered to be a 'dueling build' or 'bg farming build' of little use in a real competitive environment. It's also historically a popular build with Mage players who attempt to PVP with very little actual PVP gear - the thinking being that if they're already only useful every 3 minutes, being fairly fragile is worth it to get the most out of that 10% of the time that cooldowns are up and active. Finally, players using such a build are often considered 'cowardly' by those players who feel any sort of 'ethics' or 'honor' belong in PVP (admittedly a subset of players that attract a large amount of derision all their own), because in the intervals between cool down uses, the mage will generally use tools like Invisibility and Ice Block to avoid engaging and 'run the clock down' until their cool downs are again available.
While these perceptions are not always true (there have been times that a '3 minute mage' type build has been the flavor of the month even among the most competitive of players - generally as a source of burst damage support in team compositions that rely on other players to provide the control and durability that the mage lacks, allowing the mage to focus on fairly explosive firepower), they have been true at enough points in the history of the games competitive balance that the sterotype remains.
Alternately, it could just be that it's a euphemism for calling the player in question a premature ejaculator.