I take my small dog on the bus (X2/90 series) all of the time and have taken him (less often) on the train (even the MARC train, which has the same rule).
The mesh parts of his carrier are pretty tightly woven, so a lot of time people don’t even notice him at first. I think what usually gives me away is the fact that I’m talking to what looks to be a small tote. If people do notice him, that don’t mention it or are positive about it. A lot of people ask what kind of dog he is, whether he minds being in the carrier, etc. The only time I’ve ever had a problem is when there is a dog not in a secure carrier on the train/in the station-typically a guide dog or a police dog, though some people think they don’t need to follow the rules and just carry their pets on in an open purse/bag. Even then, it’s not a big problem, he just kind of goes nuts when he sees the other dog and people who previously didn’t notice him are a little startled when my bag starts moving!
FWIW, this is my carrier: http://www.wag.com/dog/p/petego-boby-bag-113558. I love it, but my dog is pretty tiny (about 6 lbs) and he just fits in it, so it might be a little small for your dog. I fly with my dog (in the cabin only) from time-to-time as well and before I flew with him, the vet advised me to get something that was as close to his size as possible, but that he could still comfortably turn around in-I guess it’s the same theory as the ThunderShirt; dogs like to feel closed in.
Good luck Metroing with your dog! I’m jealous that you’re able to take him to work!