I've written about this before, so a search here will turn up possibly more detailed information.
Here's the short version:
If you use your spotmeter to meter through filters (I do), then you need to be aware of the problems and how to deal with them.
First, you have to understand enough about the physics involved and how filters work to meter intelligently. As mentioned above, if you meter a red object through a red filter, the filter will have little effect on the reading. Conversely, if you meter a green or blue object through the red filter, they will read significantly darker than without the filter. Knowing which color filters pass and darken which other colors is important. Only by knowing that can you effectively place an important value for determining exposure and then find where everything else falls. So read up on color theory and study your filters so you know which wavelengths they block and pass.
Secondly, the spectral response of the meter and the film you are using likely doesn't match exactly. That means that the readings you get when reading through the filter will not translate exactly to the actual exposure the film gets or proportionately to density differences on the film for different colors. The stronger the filter, the more pronounced this effect. Furthermore, very strong filters (red, green and blue) expose only the part of the film's emulsion. Depending on how the emulsion is sensitized to different wavelengths, exposing with just one basic color can affect the contrast that the film develops to, i.e., your "Normal" with no filter might end up being N+1 or N-1 with a strong filter. This also varies from film to film.
The answer here is to run some basic exposure and development tests with the different strong filters you use (usually only red and green for most people) and the films you use most and come up with some adjustments in exposure and development. For example, 320Tri-X and a #25 filter needs 2/3 stop more exposure and a development of N-1 to get to my "Normal." So, when I meter through that filter and am using that film, I make those adjustments. Yes, I know, it's just like applying a filter factor, except I get the advantages of being able to see and measure what my filter will do in every part of the scene, something you don't get with just applying a filter factor. And, the red filter doesn't behave the same way with TMY, so I have a different set of adjustments for the #25 with that film.
The advantages of reading through the filter, however, outweigh the trouble I have to go through to fine-tune the process for me. Not only can I get a better visualization of how the densities will actually be distributed on the negative, but I can ensure better exposure in many cases than just applying a factor.
That's not to say that one can't get good results using the filter factor. However, we must also remember that filter factors are approximations and arrived at assuming standard lighting with the aim of rendering a neutral gray object the same density with and without the filter. It really tells you nothing about how much (or little) a colored object will be affected by the filter. And, when the lighting is not standard, things become much more of a crap shoot. I like to be able to see that that blue sky will actually be darker than those green trees by getting a meter reading from both of them through the filter.
Here's an example where reading through the filter wisely will result in better results than just applying the filter factor: We ZS users place an important shadow value to determine exposure. Shadows are often lit by very blue light from the open sky. A yellow, orange or red filter will darken shadows that are predominantly lit by blue light. Just applying the filter factor does not take this into account (factors are based on neutral gray under standard lighting conditions) and often results in underexposed shadows, especially with stronger filters. In this case, reading through the filter, especially if you've done your testing, gives a more accurate reading of what the exposure should be.
Hope this helps,
Doremus