I can't weigh in on Tulum but we were on the Western cruise last week and did the Chichen Itza excursion, which we loved. A lot of the water-based excursions (snorkeling, etc.) were cancelled that day because of rough seas I presume, but at least for now it seems the security warnings are not leading to the cancellation of all the mainland excursions.
As others have mentioned, it is truly a full-day tour with limited time at the actual site (about an hour at the ruins including tour, shopping time of 5 minutes or so, and bathroom visit) so it really probably only makes sense if everyone in your group is really up for it. My kids both were super interested in the history and very excited to go. We did the Disney tour and our guide was excellent. They had ipads for everyone on the tour bus that had some interesting information about Mayan culture. They also had headsets for everyone to use at the site so you could hear the guide as he explained things--even if you ended up way in the back, which we always seem to...
As for level of comfort during pregnancy, I think that's a tougher call but don't think it's a definite no. The ferry is something to be aware of for sure. It took about 45 minutes each way and was an experience. I don't get motion sick (even on similar size ferries, whale watches, smaller boats, etc.) but I felt it a little--not sick, but dizzy. The employees continuously walk the aisles with trash baskets and plastic bags--so they are prepared. My oldest did not feel well the whole time but didn't actually get sick. Plenty of others did--which I saw, heard, and smelled (sorry to be so graphic, but passing along since it was no joke and I know many get sick when they see others get sick!). That said, we all would do it again because the visit to the ruins was really a once-in-a-lifetime thing for us. I don't think there's any way to tell who will be fine and who won't on the ferry, pregnant or not--my 10 year old son was fine while I heard many adults get sick and say they've never been seasick before. There are bathrooms on the ferry but as you can imagine, there was always a wait--i think a couple of people spent nearly the whole ride in there. Also keep in mind that we took the ferry on a rough seas day. It might not always be that choppy.
If the ferry isn't a dealbreaker, the rest of the trip is pretty mild and physically comfortable IMO (admittedly coming from someone who's been lucky enough to have just regular discomfort during pregnancy and no real medical issues). The walk to the bus from the ferry was about 5 minutes on paved, shopping district streets--and actually the fresh air was nice to shake off the effects of the ferry's movement. The bus ride (really a minivan) was about 2 hours each way, on paved highway roads. Bus had A/C and window shades so pretty comfortable (no bathroom on the bus). My daughter often gets carsick and was fine. They give you a box lunch in the morning so there was food to snack on if you wanted. Our driver stopped once for a bathroom break on the way. I've had much longer rides and flights while pregnant that were far less comfortable.
The ruin location was a couple of minute walk from where the bus dropped off. There is no shade, but the site is flat and contained in a pretty small area so not a taxing walk. You can also leave bags on the bus, so don't need to lug things around the site. We thought the site and tour was awesome. After the tour, we stopped at a couple of vendors for really no more than 5 minutes. Before getting back on the bus we used the bathrooms, which were not super clean or particularly well-maintained, but served their purpose. The driver had cold water and cokes for us when we got back and then we headed back to the ship.
Obviously, it's a personal decision about what will work for your group, just passing along our experience. Hope you have a great time if you decide to go!
. And, I felt dizzier on the ferry back--I think because I had an empty stomach. 
