Counters are "bad" in limited for a lot of reasons:
1) You typically don't have a lot of instants in a limited deck. If your opponent doesn't play a spell, you went an entire turn cycle without spending mana. Unless you're already ahead, this is bad. This is why we say that counters are only good in decks with lots of other instants; for example, in Dragons Maze draft, it wasn't hard to draft a deck with 6-7 instants/flash spells at the 4cc slot, making even "bad" counterspells like Mindstatic playable because you could just play Eyes in the Skies instead (I actually loved this deck in that format; one of the few things I liked about DGR).
2) To the above point, what this typically means is that you're "priced into" countering anything that your opponent plays or risk losing massive tempo. This means that counterspells typically trade with replacement level cards and are often unimpactful.
3) You often hear people say that counterspells are better in sealed. This is because sealed decks are usually less synergistic, less tempo based, and generally have a more uneven power level distribution. That is, they play more replacement level cards without direct synergies, but they have a few very powerful individual cards that need to be answered. Beggars can't be choosers: you'll play Cancel because it's the card in your pool that can answer your opponents bomb, and it'll answer Gideon just as easily as it will Planar Outburst or Emeria Angel. And if you take a turn off to hold up a counterspell, it's probably not as big of a deal as it would be against a draft deck.