Hey - I am a first-year DPT at UIC and I commute from Elmhurst. I would say that about 1/3 of the students in our class commute from the suburbs, 1/3 travel from other parts of Chicago, and 1/3 live near campus. Of those who commute from the suburbs, probably the majority take the Metra.
I am not the biggest fan of Metra - the monthly pass is expensive (no discounts for college/grad students) and they don't allow bikes onboard during rush hour, but that is how I am getting back and forth. The main reason is that although this method of commuting is longer, for the most part, the total travel time is very predictable. Having lived near Chicago for my whole life, driving in on 290 is not a smooth commute - slowdowns mostly around the Hillside Strangler and Oak Park and it gets quite long at rush hour and in bad weather. My biggest worry about driving is that I would get stuck in a traffic jam and even if I was not late to an exam, I might be a bit stressed or frazzled. By comparison, I can get in a little bit of studying/cramming or chilling out on the Metra.
By the way, part of your tuition & fees is for an unlimited El pass - you can't get out of paying for it. At least then you don't have a hassle of a monthly pass and it lets you explore other parts of Chicago.
If you decide to drive, the best option is the Cook County Juvenile Detention Building parking - which is a covered parking garage about two blocks away from the PT building, for $2 a day. There is UIC student parking available, but I don't know the specifics...
The walk from the Metra station in downtown Chicago to the Clinton El (Pink Line) is about two city blocks, and the El trains run about every 9-10 minutes during rush. Once you get off the Pink Line at campus, it is about a three block walk to the PT building, and shorter to buildings for Anatomy and Physiology. Many of the buildings are connected and there is a tunnel system to get around, so you don't necessarily have to be outside the entire time. Also, the El stations at either end have warming lamps, so it isn't too bad to wait for the trains.
Since UIC is in the Medical District, I feel it is pretty safe - there are tons of professional people around during the rush hours. At night, it is a little more deserted, but I never feel unsafe - and there are always nurses and doctors on shifts that take the El. There are incidences of crime at UIC, but it is mostly late at night and off-campus - I don't know anyone who has been affected, other than one classmate who had a bike stolen due to a sketchy lock. Usually, there are other classmates who are also commuting at the same time, so you can walk together. As long as you don't flash expensive electronics around and are comfortable around public transportation, you'll be fine.
The main drawback, as someone else mentioned, is that after rush hour in the evening, the Metra trains run only once an hour - that does make it a little inconvenient to stay for group studying or staying late in lab. So if I knew in advance I would be late or for Saturday Anatomy lab reviews, I would drive in.
Hopefully, this answers some of your questions - feel free to send me a private message if you have other topics. I won't kid you - UIC is very tough. We take Anatomy class with other students who are post-bacc (in a prep program for med school), so you will spend most of your time with that and Physiology during the first semester. But the faculty is very supportive and my classmates are top-notch people. Good luck with your decision!