In urban warfare, the selection and killing of targets is much more difficult than being in the open, especially since Hamas and related groups launch and then run into buildings. If you've seen Gaza, this is the most highly condensed population area in the world, so any military strike is automatically going to have some civilian casualties unless they're very lucky.
Secondly, according to both the Israeli government and the IDF, many strikes were called off because it was deemed that the collateral damage would be too high.
Thirdly, the IDF definitely has special ops, and they have been utilized in many missions, including in dealing with Hamas. However, special ops are "special", thus implying and meaning that they have only limited capabilities.
Finally, a large challenge for Israel is the same problem we had in Vietnam (I was opposed to that war, btw), namely the use of hit-and-run tactics along with the ability to blend in with the population that was used by the VC and now by Hamas. Drones help, but even they will amount to civilian casualties as we're not talking about pea-shooters here.