Use of public transportation is the highest it has been in almost 60 years in almost every American city. （正）

本句，it 指代主句的主语：Use of public transportation。

it has been in almost 60 years in almost every American city 是定语从句，修饰 the highest （the + 最高级具备了名词特征），作 has been 表语的关系代词 that 被省略。

【翻译】在几乎所有的美国城市中，公共交通的使用是近60年来（其使用）最高的。

It has been the highest use of public transportation in almost 60 years in almost every American city. （误）

it 指代错误。结构错误：It is the use of public transportation? 什么意思？