I'm sure they are making money out of it. But as a % of their overall profit I imagine it's pretty small. The thing is, with companies of that size, you chase every profit you can. Sometimes companies even run loss-leading ventures because of secondary revenue, e.g. Halfords get repeat custom for spares, servicing, accessories etc.
As vernon says, the cost to smaller companies is significant.
Condor had to
add a profit margin to the list price of my bike because the normal profit is wiped out when they sell bikes-for-work. Not sure if that's to all suppliers or if it was just Halfords (my bike was ordered through Halfords and supplied to them by Condor). The net cost to me is still going to end up at about 65% of retail so I don't care about the increased price.
Mr Paul - your comment is spot on. It's unlikely anyone will get a discount because they're already saving up to 41% on list so it's safe to assume most customers aren't going to try and haggle for further savings. Still, if you rock up at Halfords and say "I want that bike but my Company cap is 500 quid" they may discount the price to get the sale. Depends if they think you're bluffing or not.