The word “meta” is short for “metagame”. “Metagame” is a slang term that refers to a set of rules, patterns or circumstances that represent the way a given game is played by its players.
For example, skull damage is very effective, easy to come by, and able to be reproduced by a great number of card combinations. So, players often create teams that revolve around making the best use of skull damage. So, the “meta” might reflect a trend of skull damage teams.
Lets say the developers wanted to respond to this and increase armor on all units in an attempt to slow down skull damage teams. You’d likely see the metagame shift towards teams that could remove armor or ignore armor and and attack health directly.
If the developer wanted to combat skull damage by reducing its raw damage output, you might see players migrate towards teams that are ability-dependent. Players may put together teams where mana can fill up quickly so that abilities can be cast repeatedly in succession. So, those teams might consist of exploders (for mana generation), low mana cost cards, transformers, etc… The meta would shift to account for the change in skull damage.
Players are extremely good at finding the most efficient way to do something in a game. As the game changes, the players will alter their strategies. That is the “meta”.