Passport to Mexico

My first piece advice would be to contact the resort directly and see what kind of discount/package they can give you. FH and I did this for a resort near Cancun last year and again to book our honeymoon and it worked out very well. By booking the flight through the hotel as part of our package we got a sizable discount on it. Plus by booking through the hotel, we paid the same price as we would have on Expedia/etc but they gave us extra goodies...coupon for $50 off at the spa, $100 discount on Chichen Itza tour, etc. They were even running a special so if you paid for 5 nights you'd get a 6th free, which we wouldn't have found elsewhere.
My second piece of advice is to, if at all possible, get a shuttle from the airport to your resort. Trying to deal with a taxi or renting a car when you're not familiar with reading Spanish street signs, traffic laws, driving patterns, etc is a nightmare. If you want your honeymoon to be relaxing, it is absolutely worth every cent to get a shuttle. You may also be able to get it as part of your resort package.

We went to Cabo a few years ago, but it wasn't all inclusive. We did parasailing and it was fine, not super amazing. We did a walking food tour and that was SO fun! We also went on a sailboat and went snorkeling, and jet-skied too. Those were great. We booked our room at Cabo Villas through VRBO.

We are doing the same, but got ours through Costco. It was super affordable! Can't say how it was yet since we still have some time before our wedding.

There are plus sides to booking through a travel agent. They get a lot of discounts and they have extra incentives they can offer. When we booked our first cruise we looked around, tried Expedia, etc. But we found a travel agent here who worked independently and he worked very hard to get us a great deal within our budget! Even last year, when we went to book our honeymoon, we thought we were getting an awesome deal/package, and then he emailed us an entirely different package that was 10X better and was still within our budget! It's worth looking into, at the least! It's usually free to book a consultation and ask about pricing.