Lens hoods more or less always,
When working, I have the lens caps off, and rely on the lens hoods to stop the front element rubbing or knocking on things inside or outside of the camera bag.
The same applies if I'm carrying a lens in my jacket pocket. Rear lens cap fitted but I rely on the lens hood to protect the front element.
As there aren't any downsides (usually) and it's always going to be useful to protect against flare, raindrops, damage and accidentally sticking a greasy or mucky finger on the front element , I automatically put one on. Exceptions are when it's very windy and the lens hood can catch the wind, or extreme close ups where the lens hood can stop some light reaching the subject.
Protective filters, I tend to only use in poor weather, so I'm cleaning rain etc from the filter, rather than the front element of the lens,
Some lenses, that I know I'm most likely to use in poor weather often end up with a protective filter (usually B+W ones) fitted all the time, and I only take it off when I feel I should be pushing maximum performance or think it's increasing the risk of flare. None of my "high quality" primes (Zeiss MIlvus and Nikon PCE lenses) have filters, but my 300mm and 24-120 lenses tend to have them on almost permanently. Not a carefully thought out strategy, just the way it's ended up, because of the way I mostly use the different lenses.