Since Darius kindly suggested that I copy and paste my comments above as an answer, here's my pseudo-introspection as a native speaker on a possible difference in nuance:
I think the difference dainichi and others discussed in the comment section there is due to the original meanings of the dictionary form and -teiru form. Before trying to analyze why there can be a difference, through examples dainichi gave I'll explain the difference I feel is there between the two grammatical constructions for habitual actions.
I feel the focus of 〜している is on the result, effect or consequence of the habitual action or something along those lines, while the dictionary form tends to be neutral and simply refers to the fact that you habitually do it. For example, "お風呂に毎日入ってます" would sound natural when you're told that you smell funny and should be a dirty guy who doesn't take a shower. In other words, yon may be saying, "I take a bath everyday! I'm clean! I don't smell!" But "お風呂に毎日入ります。" wouldn't fit equally well in this context. It'd be better when, for instance, you're asked to name one thing you do everyday, i.e., some sort of neutral question.
The same goes for the 毎年田舎に帰ってる v.s. 毎年田舎に帰る example dainichi brought up in the comment section. The former is good when the topic of your conversation is about how the family is important to you and how you love your parents, for example. Or maybe the situation is like someone wrongly accused you of being very cold to your parents, not taking care of them, not seeing them for many years etc. You're responding to the accuser by claiming that you visit your hometown every year (and thus see your family on a regular basis). The dictionary form would be more suited if you get a neutral question such as "What do you do during the holiday season every year?" If you reply by the 帰ってる version to such a question, people would expect something that follows as a consequence of it, e.g., だから他には特に何もしません.
I think the reason they have this difference is simply because, regardless of whether it's habitual or not, you use 〜ている when you're talking about things that are taking place right now in a sense while 〜する is used when you're seeing the action referred to by the verb from a certain distance on your mind. If the context dictates that the speaker is talking about a habitual action, it simply adds the habitual sense to the normal meaning.
So, 〜する can be "I will do (in the future)" or "I do (everyday)." Either way, you're mentally looking at the action from the distance kind of objectively.
By the same token, 〜している can mean "I'm doing this right now (literally)" or "I do this everyday." And in either context the speaker is feeling the action very close and think it's actually happening in a literal sense or in a figurative sense. If it's figurative, you're still thinking of what's happing as a result of this action, rather than objectively talking about the action itself.
So the short answer is that, yes, there is a difference. But it's simply the usual difference between the dictionary form and -teiru form; it's how close you are feeling the action is on your mind.