Yes It is very easy to Bot Cata mats for gathering and shuffling. Not much different than doing Panda Shuffle.
Questing run can also be good but I do it this way: Get a level 80 (SoR or RaF etc). Then use one of the various methods to bot 80-90 using Pet Battles (I use triple Mini-Mindslayers on No-no). What that does is means you hit 90 without ever doing a single Cata or Panda quest. Now you do all the quests with a 90, making them much easier and faster and get I believe, double gold reward because you no longer get the XP reward for the quests. Questing this way, more gold reward, faster questing time..more profit.
I have been told dungeon farming can be profitable if you know what to do and where and depends on your server market conditions etc. I do not do a lot of it though. Never found it to be that profitable and subject to RNG.
I do about 50K a day. I am only really doing Mop shuffle, Cata shuffle and Thorium shuffle along with selling into all the markets properly with TSM. I also find great profit in selling the plate Dreaded 458 crafted PVP gear. Ornate rings from the Mop shuffle that proc blue...also good money.
I used to chug along at 10K a day but once I really expanded my thinking...quickly grew to the 40K to 50K a day.
Really though, the secret is to really understand your server, the current market, be diversified and selling into all markets you can, be patient and build healthy stockpiles of inventory so you always have the mats on hand for when prices in one area rise due to short supply.
I do not flip blues and such, lots of people do say flipping items works great, but all it ever seems to do for me is I end up sitting on a bunch of rare items that hardly ever sell.