Because of it's significance in history or in architecture. Fenway Park is considered a icon yet you wouldn't even see it unless you're up against, in it, or flying over it. South Station is also iconic. Elsewhere, Penn station is another iconic structure that isn't tall. Neither is Madison Square Garden. The Louvre...I can go on.
Please do go on because I'm about to shut down all of your examples one by one.
Fenway Park - 2nd oldest baseball stadium in the country, seats almost 38,000 people per game for at least 81 home games (not including playoffs), plus has many other events. There is a reason for people to go here.
South Station - Tough to miss when all the commuter rail trains from the South/West, plus the trains from points South (such as NYC), plus the Red and Silver line all come through here.
Penn Station - Same as above, a transportation hub is naturally going to have people transporting through it.
Madison Square Garden - Similar to Fenway Park, this is an event-based structure which includes being the home of a major sports team. (if you want to call the Knicks a major sports team, ha!)
The Louvre - The world's largest museum, and among the most famous landmarks in one of the world's largest and most famous cities. How is anything in Kendall Square supposed to compete with the Louvre? Even MOFA isn't competing with the Louvre.
Basically your examples are either sports arenas (not going to happen in Kendall, and certainly wouldn't be iconic), the most historical transportation hubs in major cities (compared to what, the Kendall Square T stop?) and possibly the world's most famous museum. How do ANY of those apply to the potential uses here?
And yet the biggest attractions in Boston is not the Prudential or the John Hancock Tower, they are the Boston Common/Public Garden, Faneuil Hall, Fenway Park, Newbury St. In fact, look up the top 10 attractions in Boston and the Prudential Tower and John Hancock are literally afterthoughts.
I'm not saying they are necessarily the attractions. The Hancock in particular, since it closed its observation deck, has nothing to provide to the public from that perspective. What it does provide is a visible sense of place. You can see it from afar and know that Trinity Church, Copley Square, Boston Public Library, and Boylston Street are all right there. See the Pru and you know that the Hynes is by there, and the reflecting pool, and the Pru Mall. These are the visible landmarks that help you find the shorter destinations in between. Get a Hancock or Pru sized building in Kendall and it would do the same thing. One could see the huge building and immediately know the space it occupies. For Kendall in particular, this would be a positive, since it's basically a blob of fatties between 150'-300'. What better way to orient yourself than with something that stands out?