It's not just special effects but the sheer scope of the productions. You simply didn't have special effects extravaganzas in the 1990s until around 1997 or 1998 when CGI started taking off. You had films like Starship Troopers and X-Men and Phantom Menace--you simply didn't have films like that before. There is no comparison you can make, until you go back to the similar boom in the late-70/early-80s but even those were on much smaller scales. You never had action scenes with as much explosions and physical stunts as in Michael Bay's Transformers, and you rarely had films with as much prominent and as many visual effects as that film has. So, it's pretty hard to make a comparison to film cost of the past--films simply weren't that big, with rare exceptions like Apocalypse Now, but even that film only has one humongous action scene.
If you compare movies of the 2000s with those from the 90s with similar scope you see that the budget is not wildly different. Fincher's Girl with the Dragon Tattoo cost about 90 million. In 1998, Ronin cost about 75 million in todays dollars. They both in my opinion have similar scope, Ronin has more action scenes but Dragon Tattoo has more locations and a bit more ambitious story, but they are useful comparisons. Movies do cost more money these days, partly because of an increase in actor/director/producer perks and partly because film equipment is more expensive than it has been in the past (excepting the cost of celluloid itself, which is now being phased out, but then replaced with more expensive cameras in most cases), and partly because star/director/producer salaries have gone up overall.
But if you look at the only other time in history vaguely comparable to today--roughly 1978-1983--you see that those special effects blockbusters have similar cost to today. Star Trek:TMP cost $35 million in a day where a typical Hollywood A-list drama like All the President's Men cost only $7 million. So if today a typical A-list drama like Social Network costs $40 million, if you apply the same ratio (1:5) that gives you $200 million for the blockbusters of our time, which is pretty accurate. Nowadays, there are more special effects than in the 70s and early 80s, so the cost is more, plus today blockbusters are usually brand franchises with licensing fees and long development periods, so they often surpass the $200 million mark. There are even more extreme examples in the past--Cleopatra, in 1963, was a huge, huge film, like Troy or Alexander, the type of films they might make today, and that cost $45 million in a day where a typical film cost about $1 million or $2 million and an action film like The Great Escape cost $4 million. If we peg a typical film costing $2 million in 1963 and $40 million today, making Cleopatra in 2012 would be like making a blockbuster with a $900 million budget. And the film made profit too! It's remembered as a bomb but it seems to have grossed 20 million more than its budget (quite a big difference back then) by the time the decade closed.
