It was. Wasn't the Atari's CPU 1.79MHz (3.58Mhz NTSC clock/3)? The NTSC C64 was close to 1Mhz. But it's worse: The C64's CPU was also slowed down by the VIC-II every 8 scan lines to fetch video data, and slowed down additionally if sprites were enabled.

The PAL C64 was actually slightly under 1Mhz but you had a lot more VBlank time to do stuff.

The C64's CPU wasn't slowed down much at all by the badlines, less than a few percent. I'm not sure how much the sprites slowed it. The Atari was faster but how much it was slowed by depended on the video mode. Higher res and higher colors slowed it more, leaving the CPU at around 1.3 MHz. I also don't know how much the Atari player/missile graphics slowed the CPU.

The graphics chip on the Atari also steals CPU cycles, but if you use the 160x100 mode (instead of 160x200) then it can run full speed which means full 1.79MHz no questions asked.

The lower resolution also means less time plotting pixels so for any sort of software rendered effect the Atari machines are miles ahead.

Atari's CPU was slower in PAL countries, but I don't recall what the speed was. (speed based on something in PAL like the NTSC color clock, but I don't recall what it was called)