I spend a lot of time on the trains myself and understand what you mean about the expense. You've calculated them up and stated, "...I spent more than $1,000 on the subway...." then later in regards to those who work from home 100%, "...They basically get a bump of several thousand while I am wasting my money on the subway!!"
Big difference between just 'more than $1,000' and 'several thousand.' At this time since you do still need to be in the office a majority of the time you will have commuting costs no matter what whether it is living closer which will incur moving costs, etc. Cycling which means a bike with maintenance, a car with maintenance, parking, etc. Each of these options needs to be weighed $ for $ against each other as much as possible.
What do you do with your time on the train? This is valuable "oldtoyota" time! Make it work for you. I crochet on the train and sell the items on the internet or through galleries. Or sometimes I read a book to relax.
But what would be valuable to you? Writing that book you've always wanted to? Creating great slideshows of your family photos on your laptop? Reading an inspirational book? Playing Angry Birds? For your commute time, someone else is doing the work of getting you home or to work. Use it wisely and that $1000+/year may be less expensive than you think :)