Car : euro 0.4/km, travel time into brussels during heavy traffic : about 50 minutes, 30 if I'm willing to work 6am-3pm (I'm not). 21 (working days per month) * 35 (kilometer) * 2 (there and back) * 0.4 = 580 euro/month, 700 if you finance it using a loan (I don't need to). This pays for a comfortable "monovolume" car (big enough for a family, but certainly not a big car by Belgian standards). Note that this effectively comes with all sorts of bonuses, greater comfort, protection from the weather, and much cheaper and quicker groceries. I don't need parking where I work, but if I did it'd be another 50-100 per month everywhere except the European quarter. If we're talking a company car (tax deductible for companies in Belgium and thus very common), cost drops to 200-300 euros, and some companies (ie. if you're willing to do IT consultancy), drops to 100-300, depending on car, deducted from pre-tax pay. This is assuming the car's value goes to zero over a period of 4 years, whereas in practice I've always sold my cars for between 3-4000 euros after 4 years.
Public transport travel time : at least 2 hours (mostly due to waiting). Cost of bus card + train card (for one trajectory only during week days) = 150 to 300 euros (bus, depending on whether you need bus in one or two cities, so if you can get from home -> station without bus or from work -> station without bus, it's 150, otherwise 300. For me it's 300), plus 150 for the train. Add to that the cost of various other trips that you'll need to make that aren't covered by this, but are covered by having a car, and you easily get to 600 euros per month (groceries, going to town, visiting people, ...). Since I drop off kids at school using the car, if I included the cost to do that using public transport too, it'd be over 700 (2*60 euros per month to have the school bus pick them up on a street where I would worry every day they they might get killed, plus it would prevent me from leaving for work until they are on the bus).
Oh, and for that price, you get this : https://pbs.twimg.com/media/By62kxwIAAAX3Om.jpg:large
It's not a contest. Car is way cheaper, even disregarding the difference in comfort. Is that because of government subsidies for the car ? Yes. Otoh, the government also sponsors the mass transit quite a bit. How does it stack up in "real" costs ? I don't know. How much would the other disadvantages of using public transport add up to ? Don't know, but I don't think it's zero. (much less free time, less time working because of the kids limits, ...)
Of course it depends on the trajectory you take. If I had to "cross" Brussels (east-west or north-south), I'd take the train, and I know people who do so, but I'd also find another job or move, because it's simply not doable.