I am encountering the same error; all other UARTs are working, using Nucleo-L4R5ZI. USART1 CR1 remains at 0, even after the MODIFY_REG instruction is issued during initialization. I suspect that this has something to do with USART1 being on APB2 while all other USARTs are on APB1.
By manually calling __HAL_RCC_USART1_CLK_ENABLE(), I can see that USART1 CR1 is now changing to the expected value (one would not think this step necessary, as this happens in HAL_UART_MspInit as generated by CubeMx prior to any configuration being attempted).
I am still not getting transmissions through USART1. I can confirm that all registers are identical between USART1 and USART2; USART2 is working as expected. I have confirmed that the pin I am using for USART1 is functional when used as a GPIO in output mode.
The line does not idle high as expected; it is just constantly low.
I can confirm that USART1 is enabled in APB2ENR and NOT in reset state in APB2RSTR.
For all who are experiencing this issue, upgrading to the latest version of STM32CubeIDE (1.5.0) successfully resolved my issue. I was previously using 1.3.0. I presume this error was caused by some issue in the CubeMX-generated initialization code.