Yes usually it is but I did all my calculations before taking the deal and it's cheaper without the fee over the 5 year period. If the difference between the two rates was greater than 0.18% the fee one would've been cheaper.
If I had taken the 3.89% rate when it was available, which had a £999 fee, that would've saved me £2k over the 5 year period. I really can't see them getting that low again for some time.