I love debates like this, comparing eras and cars.
1994: As others have said, Williams were hurt badly by how late the regulation change banning active suspension and other driver aids for 1994 came in 1993. Their 1994 design would have been well underway. Even in the Senna film you can hear Senna saying to Newey how unbalanced the car was; understeer on entry AND mid-corner oversteer, a nightmare combination. Newey later admitted that they initialy cocked up the fundamentals of the suspension design and the height of the front wing, almost because they'd forgotten how to work with conventional springs and dampers in their 'active' years. For a Ford V8 Benetton to be faster though raises questions; yes Schumacher was extremely talented, but the potential for electronic shenanigans was likely there. Benetton's fuel rig doctoring was also a factor; how often did Schumacher pass the Williams cars via the pits? The Benetton was obviously optimised for Schumacher though; look how both Verstappen and Lehto struggled in the sister car.
1995: Yes, the Williams was much improved, but then again so was the Benetton. I still think the Williams was not quite as refined as people think, and Benetton now had the same engine as them, in a winning chassis and driver combination.
1997: The Ferrari was plainly inferior to the Williams, no doubt. Schumacher also had the problem of the rise of McLaren (courtesy of Newey) also stealing wins and points.
1999: Who knows what might have happened? That Irvine came even close speaks volumes for the quality of the car. Hakkinen did his best to throw it it away mid/late season (Monza anyone?) and you had Jordan at their peak nicking wins too.
2000: An epic battle with two teams and drivers at the height of their powers.
2001: With greater reliability, either Williams or McLaren should have taken the championship. The Williams in particular was a beast when it worked.
2003: Arguably Williams or more likely McLaren (Kimi) should have won the championship. That mid-season rule change for Michelin really shafted both teams, and swung the pendulum back to Ferrari.
2005: Bridgestone cocked up their tyres. McLaren cocked up their car. Kimi should have won, but instead kept breaking down (or flat-spotting his tyres!) Alonso won by good drives, but also good luck and good reliability.
2006: Alonso really won on merit (much as it pains me to say so, as I never warmed to the bloke). The mass damper rule change, and the Monza penalty thing was shady meddling by the FIA
2007: Conspiracy theory; due to spygate, McLaren were forced to try and shaft Hamilton at Malaysia with his tyres, and when he was still in with a shout at Brazil, introduce an engine 'glitch'... (I'm joking, or am I!)