I do like places that have "free" shipping, you know there will not be any surprises. As said, M-C is good for having just about everything, and it is quality stuff. They are the fastest shipper I know, I've been amazed at having stuff delivered less than 24 hours after I order it. They do seem to be on the more expensive side though, so I don't order too often from them.
OTOH, there are places like Amazon with "free" shipping that takes a week to get out of their warehouse. I do like, however, like Amazon Prime since it's two day "free" shipping and pretty reliable. But, I almost always make sure the prices are competitive. Sometimes a good deal, sometimes not.
As for the OP's difference in estimated vs actual shipping, you might give them feedback to let them know that you are unhappy with the inaccurate estimate. Since they are more of an industrial supplier, most of their customers probably never notice, or care.