Look at maps and aerial photos of the South End from South Station to Back Bay Station and from Boylston at Massachusetts Avenue all the way to West Newton. The only places "improved" by I-90 were the Back Bay rail yards where the Pru now stands.
Lurk and Ron -- yes the Pike did cut through parts of Newton just as Rt-2 still cuts through parts of Arlington, Belmont, Lexington with few crossings and Rt-128 cut through Lexington, Waltham, Burlington. Woburn, etc. with even fewer crossings.
However, without those highways and the others we wouldn't be able to talk about Boston as one of the leading centers of Innovation on the planet.
The entire development of Rt-128 came about when the Commonwealth converted the numbered route which had been streets running through cities and towns into a limited access highway passing mostly through open farm land. In the 1930's a major intersection of Rt-128 was the corner of Mass. Ave. and Waltham St. in Lexington Center less than 100 yards from the Minuteman Statue.
see for instance:
http://marksardella.wordpress.com/2008/05/09/route-128/
I'm sorry -- romantic attachments to rail are all fine and good -- But it is the automobile and trucks and the mostly Post-WWII superhighway network which created the 20th Century economic growth in the US.
How -- because it freed us from the dependency on rigid infrastructure.
Since the superhighway's advent a company can create itself in the woods of New Hampshire up Rt-3 and in a week it is able to ship products globally, and have people travel to/from the rest of the world through the expedient of taking a 1 hour or so drive to/from Logan.
Was the process of building the Eisenhower Interstate System and supporting highways perfect -- certainly not -- just as the creation of the rail net in the 19th Century enabled the spread of the Industrial Age but separated neighbors, polluted and darkened cities, etc.
Can we improve things -- certainly -- just as we took dozens of independent stations and combined them into things of beauty and utility such as South Station
But let's not create a revisionist history and romanticized view that had we just kept the transportation infrastructure which existed in (1930, 1940, 1950, 1960 - pick your favorite era) that we would live in Utopia, the Elysian Fields, or whatever -- we might be living in another Buffalo where the city will pay you to physically remove a house from the city limits.