There's nothing wrong with not 'understanding' certain films. Legendary directors, such as Michelangelo Antonioni or Andrei Tarkovsky, have said that you can ruin the magic of film by trying to understand it too much. What are you trying to 'understand'? Are you trying to understand what the director had inside his mind when making the film? If so, I think that's unnecessary. Movies mean different things to everybody, so it should be more about how it affects you, rather than trying to find some 'objective' meaning. However cliché it sounds, some films are meant to be more of an 'experience', rather than some linear, easy to comprehend story.

Take Synecdoche, New York for example. After my first watch, I really didn't know what the hell happened, and was kind of frustrated as a result. Yet I was constantly thinking about it, the film was moving, and it stuck with me for weeks on end. I understood some basic themes/motifs, such as the inevitability of death, or accepting one's fate, but other than that I was pretty lost. But I didn't care. I loved what I had seen. So I watched it again, and again, and again. Never underestimate the power of rewatching a movie many times. I didn't think I could latch on to any more than what I had after my first watch, but much more is now clear to me. And ot repeat that, it is clear to me, and it is how I've interpreted it. Not some semi-objective viewpoint that you could likely find when google searching "Synecdoche, New York analysis". And that's okay, I think. I still am confused by some of the films you mentioned, like Mulholland Drive, Synecdoche, New York, and The Tree of Life, despite repeated viewings, yet I always learn or have something to think about when I decide to put them on again. The Mirror is probably my third or fourth favourite movie of all time. But if you told me to tell you why Tarkovsky chose the shots he did, or what this or that symbolized, I probably couldn't tell you. But I don't really care, to be honest. It affected me deeply, and that's what matters to me.

I think you have to embrace your frustrations. A few years ago, when I really started to get into film, Mulholland Drive was one of the wackiest, most undecipherable movies I had ever watched. And I hated it because I didn't 'get' it. So I spoiled myself and immediately looked up an analysis and read everything there was to understand about the movie. I confused being intrigued with frustration, and I realized this when I started to watch more 'difficult' movies.

Now, if you just feel no gravitation towards a movie like The Tree of Life, then so be it. You didn't like it. Give it another chance in a few months, maybe, and see how your opinion changes. What ends up happening with me, is that I usually will watch a movie like that and be confused, and not necessarily know if I liked it or not. This happened specifically in the case of The Tree of Life. I watched it and felt indifferent. However, a couple months later, I got this sudden urge to revisit it. I remember how beautiful a film it was, despite my lack of understanding, so I watched it when I had the time. It blew me away on my second watch. The creation of the universe sequences were ten times more beautiful than I remember (I stand by those sequences being probably the most beautiful shit I've ever seen in a film), I latched on to the (lack of a) plot much earlier, and just overall appreciated it way more than I did my first time, and absolutely loved it.

Also, understanding what makes a movie great, versus how much you liked the movie should be exclusive from each other. You can probably read entire books about Taxi Driver, but if you're not enjoying the experience, then there's nothing wrong with that. Film is subjective. I would never scoff at someone who prefers The Avengers to The Conformist. However, if you want to, then you should make an effort to understand what makes a particular film so great. You're obviously interested in why you feel this way, so you should read some film essays about Taxi Driver or google search its influence on cinema as a whole.

Basically, not everyone is going to love a particular film. If it didn't engage you all the way through, then that's perfectly fine. If you also didn't understand anything the film was trying to say, then that's fine too. To answer your question: it is okay to not quite understand why a film is so great, if you're not going to use that same lack of understanding to say that it was a bad film. You can still appreciate a film, but not like it. Persona has never been one of my favourites, yet I can appreciate what Bergman did, and what the film achieves. I can't say I like it though.