I'll briefly go over the three main stages people complain about for my take on why they're not really that terrible:
Marble Zone - The main flaw with this level is it's slower pacing. It involves a lot of careful platforming and being forced to wait with little opportunity to go fast for longer than 3 seconds. While it goes against what you are taught in Green Hill, if you play through this level patiently without trying to speedrun it, it's a pretty chill stage that's less threatening than it looks so long as you remain careful and think ahead.
Spring Yard Zone - For the most part, nobody takes issue with this level. There's just two things people don't like: The rollers are fast and can easily hit Sonic, killing your momentum and making you lose rings. The vertical platform elevators are slow and force you to wait around. Other than this, it's pretty easy to stay in a spin state for most of the level and gain some mad speed and airtime.
Labyrinth Zone - Sonic moves slow underwater and is at risk of drowning, accompanied by the infamously stressful drowning music. For the most part, progressing through this zone with the same mentality of Marble Zone makes for a much better experience. Rather than being reckless and skipping bubble spawners to get through the level fast, make deliberate use of the bubbles every chance you get while being very careful and deliberate with your platforming, careful not to fall into any of the various traps laid out for you in the zone.
The common theme in each of these zones is that they force Sonic to slow down, which is what people don't want to do while playing Sonic. It is admittedly a problem, and is something they probably should have thought through better, but at the same time I feel like people overstate how bad these zones really are. I've felt mildly annoyed by them, but they never genuinely frustrated me or made me want to stop playing (aside from on the GBA version).
Sonic 4 on the other hand is an example of level design that can be genuinely frustrating. Lost Labyrinth, the Labyrinth Zone equivalent, is actually worse than the real Labyrinth Zone for all the wrong reasons, and singlehandedly makes me want to uninstall the game every time I play it. Sonic 4 overall has mediocre graphics and feels genuinely worse than most fangames in every other way unlike Sonic 1 which still holds up quite well, even the original Genesis/Mega Drive version. The level design in Sonic 4 episode 1 feels a lot like some kid with no understanding of level design made a romhack with basic platforming, with the occasional badly placed enemy mixed in to screw you over and puzzles that are usually neither fast nor fun. Episode 2 does a bit better, though Episode Metal is everything wrong with Episode 1 on steroids.
Overall Sonic 1 may not have the refined level design and pacing of it's immediate sequels, but I'd not hesitate to say it does better than many people give it credit for and it still holds up as a great game today.