I currently commute 3 days a week having moved to Winchester when my DC1 was the same age as yours. It's not to be compared with my previous 30 min walk to work - was lucky enough to both live and work in the City - but it does have its advantages (mostly the chance to catch up on sleep - I now have two small DCs).
The main downside for me is the cost. I pay just short of £400 per month, which never ceases to make me shudder. Snow days aside, when SW Trains never fails to fall to its knees, the service itself is fairly reliable (although trains are often ten minutes or so late into Waterloo/Winchester due to congestion/signal failures/a suicide) and peak time services are very frequent.
Some trains are much more crowded than others, especially if you want/need to catch a non-stopping (i.e. fast) service that leaves in the 6.30am-8am window. I tend to catch the 6.55 or 7.55 stopping service (only 10 mins more than the fast one) and often see people standing on the fast service that leaves 5 mins earlier. Touch wood, I always get a seat.
I don't think I'd like to do it 5 days a week (and, in fact, soon won't be doing it at all, which was always the plan) but, if I had to, I could. Lots of people do.
Actually, now I think about it, one of the main drawbacks is childcare. It's not too bad if you have a nanny but most people I know juggle the commute with nursery pick ups and drop offs, which must be hard. More than once, we have collected a friend's DS from nursery because she has been trapped on a slightly delayed train. If you'd be using a nursery, having that kind of back up is, I think, essential.