I don't think "it probably infringes software patents in the US" is a reasonable argument against using a specific piece of software. Aside from the arguments against the legitimacy of software patents, it's practically tautological to say that non-trivial software infringes on patents, somewhere.
Here's the problem with that line of argument: while it may hold true for software patents, when it comes to online video one of the fastest growing categories of end-users are people viewing video on mobile and embedded devices. These devices use dedicated hardware to decode video without killing the available power budget. If there is anything behind the claims that WebM infringes upon MPEG-LA patents then you are not going to see the lawsuits drop until real devices are shipping with dedicated hardware decoders. Such devices are easier to nab at borders and by getting an injunction against the importation of these devices the MPEG-LA would also start the process with an action that will directly hurt the bottom-line of the alleged infringing party.
If I understand correctly, the h264 license would protect these device makers from lawsuits since the devices probably decodes both h264 and WebM. Thus they already have a license to the patents and the MPEG-LA can't do anything about them.
I don't think that's the argument being used. I think the argument is that there is no reason to believe that you are less likely to get sued for using WebM than if you use h.264. If you use WebM, there's just a bit more uncertainty about who will sue you.
