It's not a stupid question at all! But the temple ruins at Largo Torre Argentina are actually better protected from random brick-grabbers than the outside of the Colosseum, most of the Roman Forum, and the Theater of Marcellus, the Porticus Octaviae, or any other ground level ruin.

Largo Argentina is below the modern ground level, and is only soon being opened to the public (a recent article on the plans). It has always (well, not always, but since being dug back up ca. 1927) been something to look at, but not something you could go scramble around on--it's also a very busy area and someone would notice if you tried. It is a kind of museum, an open air preserved archaeological site, where it's a big old pit in the middle of a road that you can look down into and read some placards about on the fence. Similar to the *Ludus--*the gladiatorial school, or the imperial fora.

Your question about preservation hits on the ultimate problem in archaeology: it is, as my first field instructor once said to me "the art of controlled destruction". Aside from tearing apart the layers of the earth to get inside, once you open something up to the elements--take it out of the ground--it's going to start decaying more quickly, so there is always a balance to be struck between public accessibility and preservation. Many archaeological sites, if they aren't pretty spectacular to look at, are reburied to keep them safe. Those that remain open must be conserved--consolidated by new building materials, columns re-erected, gaps filled in to keep everything upright. Conservation is a whole fascinating field in itself.

You're absolutely right that the site is very historically significant, and the importance of Largo Argentina goes beyond Caesar's assassination there. The "manubial" temples--the four excavated small temples you can see there--were the results of vows by military commanders in the Republican era in honor of their successes. Temple B, for example, was probably vowed by Quintus Lutatius Catulus ca. 101 BCE after the Battle of Vercellae, where he stopped an invasion of the Germanic Cimbri up in what is now northern Italy (Eleanor Leach's 2010 article on JSTOR discusses this) . The practice of vowing manubial temples was one way in which victorious generals during the Republican period could display the proceeds of their triumphs, as well as establish their legacies by permanently monumentalizing their accomplishments on the landscape of the city. Together, they form little architectural snapshots of the development of this area, and the ways that commanders chose to monumentalize their triumphs, from the third-first centuries BCE.

Pompey's theater itself, the first permanent theater in Rome, just grazes the site (this is where the Senate was meeting when Caesar was killed), and is also significant as an example of the ways that very ambitious Romans could bend the norms of society to their benefit. Stone theaters had been banned in Rome, so Pompey placed his a.) outside the sacred city boundary called the Pomerium and b.) put a little temple to Venus on top of the theater and so was able to publicly claim that he had dedicated a temple with a theater on its steps--much more noble and pious to satisfy the moral authorities, but also popular with the theater-goers!

The four temples that you see at Largo Torre Argentina stood just in front of an enormous portico in front of the Theater of Pompey (the front steps of which were where Caesar supposedly fell at the feet of Pompey's statue). I've been trying to find a map that shows this clearly and this blog seems to show it best. You can see the four visible temples highlighted in red; the yellow background shapes show modern city blocks. The theater of Pompey was a large enough complex that parts of the foundations of its curved cava are visible today in the lower floor of a restaurant, Ristorante San Pancranzio, about three blocks away. If you look at the area on google maps you can see that all of the modern buildings in that area still follow the curved outline of the theater's foundation, as do the roads.

Only the very outer edge of the theater complex is visible in Largo Torre Argentina--most of its ruins remain buried below the modern streets.

On a last note, the cat sanctuary is lovely--the cats can roam the site, but there is also a shelter built into the side (near the tram tracks) that you can visit and learn all about the work they do and even meet some of their more delicate special needs kitties that stay indoors. Highly recommend!