First note that only about 30 roots in Esperanto have an explicitly male meaning. These are mainly the familial roots like "patro", "filo" and "edzo", nobility roots like "reĝo" and "princo" and a handful of others, like "viro", "knabo" and "monaĥo". Most other roots for naming people, e.g. profession roots like "piloto", "kelnero" and "studento", nationality roots like "germano" and "ĉino", and many others, like "amiko", "najbaro" turisto" etc. are not inherently male, even though traditionally there was a strong habit to add the suffix "-in-" whenever talking about a specific woman, so that when used in the singular to talk about a specific person known to the speaker, these words without the "-in-" suffix would often have been understood to refer to a male. However, this habit is already fading slowly for some decades, so that they are becoming even more neutral than they already were in the early days.
As for the 30 explicitly male roots: There are only very few people who use them with a gender-neutral meaning, and use "-iĉ-" for the male meaning, mainly some young Esperanto speakers in some Western countries. This usage is called "iĉismo", and is often combined with riismo, the usage of "ri" as a gender-neutral pronoun. Iĉismo can bring about misunderstanding, as most people would understand "patro" to mean "father", no "parent". (However, one of the active user of iĉismo has written on Facebook that he is rarely misunderstood in practice.)
I consider the lack of a gender-neutral word for "parent", "sibling", "spouse" etc. in traditional Esperanto a serious problem. After thinking hard about this problem for a long time, I have concluded that the best solution is to use the prefix "ge-", which traditionally only meant "of both genders", also in the sense of "of any gender", i.e. use "gepatro", "gefrato", "geedzo" etc. as gender-neutral terms for "parent", "sibling", "spouse" etc.
In my article "Esperanto kaj sekso" I have written about this problem (and the related issue of a gender-neutral pronoun) in great detail: http://lingvakritiko.com/2014/10/16/esperanto-kaj-sekso/ (But note that when I wrote that article, I didn't yet favour the idea of expanding the traditional meaning of the prefix "ge-".)