Possibly to avoid 'temporal contamination'
True, using a train to push the DeLorean to 88mph is risky, but consider having it go down a hill. There is the real potential that pushing it down a hill or mountain simply wouldn't get it up to 88mph in time. If it didn't and they crashed this could have disastrous consequences. Imagine the wreck of a DeLorean (not to mention a time machine) was found at the base of a mountain. If it were discovered, it could have a severe impact, not only on culture (aliens are coming!!), but also technologically (a car from 100 years into the future - pretty impressive).
Regarding the horse-and-pulley system, again this has huge potential for temporal contamination. If something goes wrong and the DeLorean isn't suspended properly, it could shoot out into plain site of a bunch of people. Again, the civilisation of Hill Valley will be temporally contaminated.
and, of course, a paradox
Also, remember that:
this sucker's nuclear
so, if it exploded and wasn't far away from the Hill Valley settlement, it could destroy Hill Valley. Then how will Doc and Marty meet, let alone embark on their adventure, if Hill Valley was destroyed by a nuclear explosion?
...but by using the train
Yes, the issue of temporal contamination still remains by using a train, but they knew it was possible to get the train up to the speed. Furthermore, if something went wrong and the DeLorean didn't get to 88mph, the DeLorean would go flying over the edge, meaning it would be very difficult to find the remains of it, reducing the chances for temporal contamination!