It has to do with the realities of a supersonic ejection at high altitudes, which is usually fatal for unprotected aircrews, both from bodily trauma from exposure to a supersonic slipstream and the extreme low temperatures and pressures which would be encountered at typical cruise altitudes.
The United States invested in increasingly faster supersonic bombers in the 1950s and 60s in order to thwart conventional defences and interceptors operated by the east bloc, so the realities of Mach 2 or Mach 3 flight demanded these kind of enclosed and pressurized escape systems in the event of an inflight emergency or enemy attack. But the realities of modern Warsaw Pact IADS using radar guided missiles made supersonic and easily detected bomber fleets an impractical investment for strategic nuclear delivery. With the return to the subsonic flight envelope and lower operational altitudes made conventional ejection seats a much more mature and realistic option for an escape system.
A good example of this was the Rockwell B-1A, which was to have used an large four man escape capsule similar to the F-111's prior to its cancellation by the Carter Administration. It's successor, the B-1B which was optimized for slower and low level penetration abandoned the escape capsule for the mature and established McDonnell Douglas ACES II ejection seats at each crew station.
Additionally, escape capsules are large, heavy, complex pieces of equipment, not to mention expensive. The F-111's escape capsule cost as much as a completed F-86 SaberJet. Complexity increases the number of failure modes and risk of failure during emergency use exponentially, requiring more maintenance, etc.
Curiously one high altitude, high speed cruiser, the Lockheed A-12/SR-71, used conventional ejection seats throughout its career albeit requiring the crew to suit up in full pressure suits during the flight. I do not believe that the seats were intended for use at supersonic speeds, leaving no means of escape for the crew during this regime of flight. This was also true of the North American X-15, a Mach 6 research aircraft where an ejection at cruise altitude and speeds would have certainly proved fatal.
Are there any side-side aircraft with ejection seats?
Yes. Multiple aircraft with this cockpit configuration used ejection seats including the B-1, B-52, B-2, A-6, OV-1, and T-37.