Help: Honeymoon trip to Switzerland and Italy (12nights)

You can look at train schedules at www.bahn.com. Zermatt-Venice is straight forward, change trains at Brig and Milan, at least one train every hour during daytime.

Buy your tickets in advance for Italian trains as these offer substantial discounts for nonrefundable tickets, which should be no problem for you as you have set schedule. Get tickets at www.trenitalia.it

In Switzerland, some type of pass may be warranted for side trips and touring as well as your main travel days. www.sbb.ch. This site will also display schedule for Zermatt-Venice.

Pick hotels near train stations and you can walk to the hotel (if you travel light). Otherwise there are local busses and taxis.

1. How do i travel between the two countries (Train preferable)?
Train is the easiest for all the trips you list. Go to www.sbb.ch (Swiss Federal Railways) for trains in and from Switzerland, trenitalia.com for Italian trains. These sites will give you times and prices.

2. How do i travel from Zermatt to Venice/Florence?
Same answer as above, train. www.sbb.ch will give you the quickest route.

3. Which rail pass is the most preferable one while covering both the countries?
Probably none. It is often cheaper to get individual tickets for each trip. Again, prices on abovementioned websites.

4. Which is the best means of travelling between station and hotel in both the countries?
Depends on how far it is. If a short distance walk.
Interlaken, Zermatt, Florence - walk or taxi.
Venice - water bus (no roads, water bus stop is in front of station).
Rome - walk, bus, metro or taxi.

The 30 day Half Fare Card for 120 chf is likely to be your best value. Your 3 main travel days will be about 177 chf per person. If you plan on some day trips on mountain railways while in Interlaken and Zermatt, that will put you over the break even point of 240 chf.
The 8-day Swiss Pass is not a good value for you at 363 chf per person. You are unlikely to spend that much, and it only gives a 50% discount on mountain railways, same as the Half Fare Card.