In my experience I would say that MFP does over-estimate cals burned cycling but not by as much as you may think (at least for me). The speed zones also play a part, eg. if your avg for the ride was 14.2mph, log it in the 14-16 zone but perhaps take a look at the same time for 12 - 14 and see how similar the numbers are. A 40min ride at 12 - 14 may say 600 in the higer band and 450 in the lower band. Perhaps put in 500, if it's only just inside the 14-16 zone.
I ride with a HRM (yes, I know it's not totally accurate either) when I go on weekend rides and did a few commutes a while ago, with the HRM on. Estimated calorie burns via MFP were a little higher than the HRM figures, probably to the tune of 20 - 25%. For this reason I always aimed to finish each week with plenty of 'exercise cals' in the bank. Infact I used to come in with thousands leftover, in the early weeks/months and this was reflected to a degree in my loss rates. Whereas MFP will allow upto 2lb / week loss tracking, I was dropping 4 - 4.5 lb per week for months on end.
Lately, I reduced my deficits as I am nearly at goal and the predicted loss rates from MFP are actually quite accurate. I still aim to have calories in the bank each week, however. I would try it for a while (a month +) and see how it works out for you. You will soon get a feel for how accurate or otherwise the estimated calorie burn is. It is at least as important to accurately record consumption. Invest £10 in an electronic food scale and be religious with logging everything you have eaten / drunk. You'll soon get into the swing of it and it becomes less tiresome to log food when you have all of your regularly used items in your favourites / recent lists.