VTOL aircraft are expensive to build, expensive to operate, have a shorter range, carry a smaller payload, and have a substantially higher accident rate than a conventional aircraft of similar size.
The US Navy reports that the AV8B Harrier has 11.4 crashes per 100,000 flight hours, while the similar in size but conventional FA-18 Hornet experienced 3 crashes per 100,000 flight hours. Keep in mind that the Hornet operates from carriers, a dangerous occupation, so the accident rate for land based military aircraft will be even lower.
A Marine maintenance officer told me that to change the engine on a Harrier, it's 400 hours work, whereas it's about 4 hours on the Hornet. Engine placement on a VTOL aircraft is critical to maintaining CG while in hover, which is why the Harrier's engine is buried in the middle.
The one advantage of VTOL (or typically STOVL, vertical takeoff severely limits the fuel and payload) is the ability to operate from a small and unprepared base. With the advent of aerial refueling, which extends the range of aircraft that need a long runway, the need for VTOL aircraft is now very limited. For short range, quick response combat support, helicopters with their superior slow/no speed flight envelope can fill the need.
The only reason to use VTOL aircraft on a carrier is if the carrier isn't large enough to support a catapult and arresting gear. For a smaller navy, it's cheaper to build a small carrier with a few STOVL aircraft, than build and maintain a large cat/trap carrier. That's the tradeoff - VTOL aircraft are more expensive, but the smaller carrier needed to support them is cheaper to build and operate.
Which makes the RN's choice of the STOVL F35B for the QE class carriers a bit puzzling - they are definitely large enough to support cat/trap, with the lower costs, better mission performance, and lower accident rates of cat/trap aircraft.