They should include flights- perhaps you were confused by the "Room Only" statement (which means there are no meals included). They'd normally include car hire, but not car insurance.
However, TCD do tend to have a lot of "hidden" charges- booking fees, credit card charges etc, plus the rate is typically based on 4 adults sharing (or there will be no discount for kids).
The other catch is that they are all "from" prices, meaning that there are a limited number of holidays available at that price. Once those seats have gone, the price goes up, often significantly (after all, someone has to pay for all the really cheap deals!).
And the dates in the article are rather vague, so you think "hmmm, October from £329 sounds good", except then you find out that the particular week in October you travel- most likely half term- is actually £300 more expensive each.